ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.7.6-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250709_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.227, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.227, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.199, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.199, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.212, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.24, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32  
Log from Wed Jul 9 09:46:30 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32  
Log from Tue Jul 8 14:43:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32  
Log from Tue Jul 8 14:25:38 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 5.81, step 1, values float32  
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  
Log from Mon Jul 7 17:31:35 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32  
Log from Mon Jul 7 09:47:13 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250705_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Sat Jul 5 20:47:49 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Fri Jul 4 14:29:17 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Fri Jul 4 10:54:24 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Fri Jul 4 09:53:55 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250703_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Thu Jul 3 17:41:19 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Wed Jul 2 17:43:06 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32  
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32  
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32  
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32  
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32  
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32  
Log from Wed Jul 2 15:03:33 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.00608, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.00134, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000955, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000493, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.00616, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00152, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.000716, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.000812, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0066, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0013, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000798, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000426, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0064, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.00156, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.000666, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.000439, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.00725, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.00154, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.000864, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.000379, step 1, values float32  
Log from Tue Jul 1 15:42:09 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32  
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32  
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.00608, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.00134, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000955, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000493, step 1, values float32  
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.00616, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00152, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.000716, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.000812, step 1, values float32  
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0066, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0013, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000798, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000426, step 1, values float32  
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0064, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.00156, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.000666, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.000439, step 1, values float32  
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.00725, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.00154, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.000864, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.000379, step 1, values float32  
Log from Tue Jul 1 13:02:54 2025 Startup Messages  
---  
warning | No presets found in custom preset folder /Users/becca/Desktop/Postdoc/Computational_references/ChimeraX_presets  
note | available bundle cache has not been initialized yet  
  

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  

> graphics silhouettes true

> set silhouetteWidth 1.5

> ui mousemode right "translate selected models"

> alias t0 transparency 0

> alias t50 transparency 50

> alias t60 transparency 60

> alias t70 transparency 70

> alias t80 transparency 80

> alias t90 transparency 90

> alias fmap ui tool show "Fit in Map"

> alias delh select H; delete sel

> alias ls lighting soft

> alias 0 transp 0; lighting soft

> alias fit transp 50; lighting simple

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> functionkey F1 mousemode right 'rotate selected models'

> functionkey F2 mousemode right 'translate selected models'

> functionkey F3 view sel

> functionkey F5 turn x 1 90

> functionkey F6 turn x -1 90

> functionkey F7 turn y 1 90

> functionkey F8 turn y -1 90

> functionkey F9 turn z 1 90

> functionkey F10 turn z -1 90

> cartoon smooth 1

> style stick

Changed 0 atom styles  

> size stickRadius 0.3

Changed 0 bond radii  

> set bgColor white

> alias bbh hide @C,N,O

> alias bb show @C,N,O

> cartoon all

> style stick

Changed 0 atom styles  

> color all byhetero

> hide atoms

> transparency 0

> lighting soft

> color name alphav1 #5786F5

Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5

  

> color name alphav2 #2A4B9B

Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b

  

> color name betapv1 #53EAF3

Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3

  

> color name betapv2 #759ED9

Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9

  

> color name betav1 #37863D

Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d

  

> color name betav2 #207B35

Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35

  

> color name deltav1 #CE8041

Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041

  

> color name deltav2 #E97408

Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408

  

> color name epsilonv1 #F06969

Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969

  

> color name gammav1 #2AFF3C

Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c

  

> color name gammav2 #61B230

Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230

  

> color name zetav1 #E0C819

Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819

  

> color name zetav2 #EFE30C

Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c

  

> color name arf1v1 #FF76AF

Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af

  

> color name arf1v2 #EB70A8

Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8

  

> color name label_red #E32723

Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723

  

> color name label_purple #6C4896

Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896

  

> color name alphav3 #57679E

Color 'alphav3' is opaque: rgb(34.1%, 40.4%, 62%) hex: #57679e

  

> color name betapv3 #7ACADA

Color 'betapv3' is opaque: rgb(47.8%, 79.2%, 85.5%) hex: #7acada

  

> color name betav3 #447A57

Color 'betav3' is opaque: rgb(26.7%, 47.8%, 34.1%) hex: #447a57

  

> color name gammav3 #ADE57C

Color 'gammav3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c

  

> color name deltav3 #E5AF76

Color 'deltav3' is opaque: rgb(89.8%, 68.6%, 46.3%) hex: #e5af76

  

> color name epsilonv3 #EB8675

Color 'epsilonv3' is opaque: rgb(92.2%, 52.5%, 45.9%) hex: #eb8675

  

> color name zetav3 #F0E07B

Color 'zetav3' is opaque: rgb(94.1%, 87.8%, 48.2%) hex: #f0e07b

  

> color name arf1v3 #EB8BCA

Color 'arf1v3' is opaque: rgb(92.2%, 54.5%, 79.2%) hex: #eb8bca

  

> color name label_red_v3 #E51A16

Color 'label_red_v3' is opaque: rgb(89.8%, 10.2%, 8.63%) hex: #e51a16

  

> color name label_purple_v3 #691099

Color 'label_purple_v3' is opaque: rgb(41.2%, 6.27%, 60%) hex: #691099

  

> color name lable_purple_v4 #9057AD

Color 'lable_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad

  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure_sharp.mrc"

Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure.mrc"

Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc"

Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc"

Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc"

Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc"

Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc"

Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc"

Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc"

Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc"

Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc"

Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 0.729, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc"

Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 0.729, step 1, values
float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_005_volume_map_bprime_local.mrc"

Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_005_volume_map_sharp_bprime_local.mrc"

Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_bprime_local.mrc"

Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_sharp_bprime_local.mrc"

Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_bprime_local.mrc"

Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_sharp_bprime_local.mrc"

Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_005_volume_map_bprime_local.mrc"

Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_005_volume_map_sharp_bprime_local.mrc"

Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_004_volume_map_bprime_local.mrc"

Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_004_volume_map_sharp_bprime_local.mrc"

Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_004_volume_map_gammazeta_local.mrc"

Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_004_volume_map_sharp_gammazeta_local.mrc"

Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_005_volume_map_gammazeta_local.mrc"

Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_005_volume_map_sharp_gammazeta_local.mrc"

Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_004_volume_map_gammazeta_local.mrc"

Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_004_volume_map_sharp_gammazeta_local.mrc"

Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32  

> hide #!28 models

> hide #!27 models

> hide #!26 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> show #!1 models

> select add #3

2 models selected  

> view matrix models #3,1,0,0,11.802,0,1,0,1.1649,0,0,1,22.807

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.42058,-0.90712,0.015978,332.41,-0.80828,0.38263,0.44752,138.26,-0.41207,0.1753,-0.89413,312.09

> fitmap #3 inMap #1

Fit map
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138102 points  
correlation = 0.9343, correlation about mean = 0.6786, overlap = 2.406e+04  
steps = 156, shift = 6.42, angle = 18.1 degrees  
  
Position of
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34036295 -0.91876592 -0.20005563 354.03277644  
-0.77656396 0.15469587 0.61075167 146.14319511  
-0.53019004 0.36323323 -0.76613324 277.46223631  
Axis -0.56713702 0.75643433 0.32582620  
Axis point 252.05264579 0.00000000 81.40495015  
Rotation angle (degrees) 167.39564073  
Shift along axis 0.16710354  
  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select add #4

2 models selected  

> view matrix models
> #4,-0.16847,-0.98434,-0.051916,308.16,-0.77209,0.099036,0.62775,149.29,-0.61277,0.14584,-0.77668,305.19

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.16847,-0.98434,-0.051916,317.82,-0.77209,0.099036,0.62775,149.66,-0.61277,0.14584,-0.77668,323.39

> fitmap #4 inMap #1

Fit map
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138119 points  
correlation = 0.9535, correlation about mean = 0.7475, overlap = 3.27e+04  
steps = 128, shift = 2.65, angle = 13.7 degrees  
  
Position of
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
(#4) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34033481 -0.91878664 -0.20000833 354.04060287  
-0.77649015 0.15464973 0.61085719 146.12650484  
-0.53031619 0.36320047 -0.76606146 277.48080009  
Axis -0.56714143 0.75641504 0.32586328  
Axis point 252.06555110 0.00000000 81.39782971  
Rotation angle (degrees) 167.38858263  
Shift along axis 0.16199507  
  

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> hide #!9 models

> select add #8

2 models selected  

> select add #7

4 models selected  

> select add #6

6 models selected  

> select add #5

8 models selected  

> view matrix models
> #5,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808,#6,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808,#7,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808,#8,1,0,0,10.109,0,1,0,2.5885,0,0,1,20.808

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41,#6,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41,#7,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41,#8,-0.27105,-0.96135,0.048324,315.79,-0.78137,0.24907,0.5722,138.42,-0.56213,0.11734,-0.81869,331.41

> fitmap #5 inMap #1

Fit map
W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138161 points  
correlation = 0.915, correlation about mean = 0.6261, overlap = 2.286e+04  
steps = 144, shift = 6.68, angle = 15.4 degrees  
  
Position of
W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc (#5)
relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33486423 -0.92026440 -0.20243362 353.69981178  
-0.77926293 0.14969047 0.60855734 147.51639631  
-0.52973128 0.36153311 -0.76725393 277.76199824  
Axis -0.56967931 0.75480327 0.32517303  
Axis point 252.70022071 0.00000000 81.39359448  
Rotation angle (degrees) 167.47826779  
Shift along axis 0.17110458  
  

> fitmap #6 inMap #1

Fit map
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138162 points  
correlation = 0.9385, correlation about mean = 0.703, overlap = 3.152e+04  
steps = 124, shift = 6.79, angle = 15.3 degrees  
  
Position of
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
(#6) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33341982 -0.92087059 -0.20206083 353.53923788  
-0.78000897 0.14906211 0.60775528 147.84755443  
-0.52954435 0.36024692 -0.76798759 277.99643882  
Axis -0.57030812 0.75458667 0.32457296  
Axis point 252.86314379 0.00000000 81.47103793  
Rotation angle (degrees) 167.46738658  
Shift along axis 0.16762333  
  

> fitmap #7 inMap #1

Fit map
W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138206 points  
correlation = 0.9279, correlation about mean = 0.6497, overlap = 2.411e+04  
steps = 136, shift = 6.69, angle = 15.3 degrees  
  
Position of
W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc (#7)
relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34035723 -0.91890040 -0.19944673 353.88927693  
-0.77660263 0.15512153 0.61059451 146.07614815  
-0.53013707 0.36271111 -0.76641721 277.57142341  
Axis -0.56711725 0.75656617 0.32555437  
Axis point 251.97967916 0.00000000 81.48001825  
Rotation angle (degrees) 167.37630205  
Shift along axis 0.18414629  
  

> fitmap #8 inMap #1

Fit map
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138103 points  
correlation = 0.9399, correlation about mean = 0.7087, overlap = 4.09e+04  
steps = 132, shift = 6.54, angle = 15.4 degrees  
  
Position of
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
(#8) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34016956 -0.91889502 -0.19979141 353.89977575  
-0.77635698 0.15454414 0.61105314 146.04451039  
-0.53061710 0.36297113 -0.76596178 277.53661238  
Axis -0.56719105 0.75636832 0.32588538  
Axis point 252.01132593 0.00000000 81.40408707  
Rotation angle (degrees) 167.36769172  
Shift along axis 0.17978067  
  

> select subtract #8

6 models selected  

> select subtract #7

4 models selected  

> select subtract #6

2 models selected  

> select subtract #5

Nothing selected  

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> show #!9 models

> show #!10 models

> show #!11 models

> hide #!11 models

> select add #10

2 models selected  

> select add #9

4 models selected  

> view matrix models
> #9,-0.20458,-0.9646,-0.16641,334.03,-0.77373,0.055221,0.6311,156.33,-0.59957,0.25787,-0.75764,298.39,#10,-0.20458,-0.9646,-0.16641,334.03,-0.77373,0.055221,0.6311,156.33,-0.59957,0.25787,-0.75764,298.39

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.20458,-0.9646,-0.16641,335.57,-0.77373,0.055221,0.6311,156.39,-0.59957,0.25787,-0.75764,301.3,#10,-0.20458,-0.9646,-0.16641,335.57,-0.77373,0.055221,0.6311,156.39,-0.59957,0.25787,-0.75764,301.3

> fitmap #9 inMap #1

Fit map
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc in
map W20_J3623_consensus_structure_sharp.mrc using 138204 points  
correlation = 0.9071, correlation about mean = 0.5649, overlap = 2.482e+04  
steps = 92, shift = 0.476, angle = 8.65 degrees  
  
Position of
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
(#9) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33561246 -0.92104503 -0.19758628 353.34320386  
-0.77965973 0.15387748 0.60700283 147.26083252  
-0.52867286 0.35776778 -0.76974491 278.24593808  
Axis -0.56920453 0.75613754 0.32289661  
Axis point 252.48560152 0.00000000 81.78647209  
Rotation angle (degrees) 167.35364255  
Shift along axis 0.06955954  
  

> fitmap #10 inMap #1

Fit map
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 138104 points  
correlation = 0.9176, correlation about mean = 0.6072, overlap = 3.365e+04  
steps = 96, shift = 0.462, angle = 8.63 degrees  
  
Position of
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
(#10) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33524620 -0.92121016 -0.19743815 353.30178908  
-0.77963330 0.15360588 0.60710555 147.28662723  
-0.52894414 0.35745918 -0.76970191 278.32308895  
Axis -0.56934667 0.75603676 0.32288198  
Axis point 252.53350589 0.00000000 81.77924134  
Rotation angle (degrees) 167.33564064  
Shift along axis 0.06841760  
  

> select subtract #10

2 models selected  

> select subtract #9

Nothing selected  

> hide #!9 models

> hide #!10 models

> show #!11 models

> show #!12 models

> volume #11 level 1.414

> volume #12 level 1.511

> select add #11

2 models selected  

> select add #12

4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.12102,-0.028286,0.99225,32.717,0.99084,0.056881,0.12247,-30.578,-0.059904,0.99798,0.021144,3.463,#12,-0.12102,-0.028286,0.99225,32.717,0.99084,0.056881,0.12247,-30.578,-0.059904,0.99798,0.021144,3.463

> view matrix models
> #11,-0.047287,-0.19762,0.97914,47.757,0.3239,0.92424,0.20219,-66.044,-0.94491,0.3267,0.020305,232.25,#12,-0.047287,-0.19762,0.97914,47.757,0.3239,0.92424,0.20219,-66.044,-0.94491,0.3267,0.020305,232.25

> view matrix models
> #11,-0.88887,-0.45801,0.011781,346.86,-0.23966,0.48671,0.84005,-8.5049,-0.39048,0.74387,-0.54239,168.45,#12,-0.88887,-0.45801,0.011781,346.86,-0.23966,0.48671,0.84005,-8.5049,-0.39048,0.74387,-0.54239,168.45

> view matrix models
> #11,-0.19168,-0.96873,-0.15754,339.31,-0.75924,0.044642,0.64928,159.39,-0.62194,0.24407,-0.74406,302.98,#12,-0.19168,-0.96873,-0.15754,339.31,-0.75924,0.044642,0.64928,159.39,-0.62194,0.24407,-0.74406,302.98

> fitmap #11 inMap #1

Fit map
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc in
map W20_J3623_consensus_structure_sharp.mrc using 42734 points  
correlation = 0.9154, correlation about mean = 0.4456, overlap = 5.735e+04  
steps = 104, shift = 9.56, angle = 10.3 degrees  
  
Position of
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc
(#11) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34146109 -0.91804101 -0.20150685 354.32329233  
-0.77726306 0.15526879 0.60971610 146.26157419  
-0.52845666 0.36481815 -0.76657763 277.10408311  
Axis -0.56679376 0.75669526 0.32581761  
Axis point 251.95105256 0.00000000 81.46580342  
Rotation angle (degrees) 167.52357003  
Shift along axis 0.13259978  
  

> fitmap #12 inMap #1

Fit map
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
in map W20_J3623_consensus_structure_sharp.mrc using 37926 points  
correlation = 0.9185, correlation about mean = 0.4316, overlap = 5.437e+04  
steps = 120, shift = 9.52, angle = 10.3 degrees  
  
Position of
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
(#12) relative to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34132328 -0.91808135 -0.20155652 354.32310537  
-0.77719944 0.15505915 0.60985055 146.27901701  
-0.52863923 0.36480581 -0.76645762 277.14013363  
Axis -0.56684797 0.75662172 0.32589408  
Axis point 251.98254766 0.00000000 81.45327260  
Rotation angle (degrees) 167.51718440  
Shift along axis 0.14887713  
  

> select subtract #12

2 models selected  

> select subtract #11

Nothing selected  

> hide #!1 models

> volume #11 level 1.414

> hide #!11 models

> hide #!12 models

> show #!13 models

> show #!1 models

> show #!14 models

> fitmap #13 inMap #1

Fit map W20_J4021_005_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138166 points  
correlation = 0.8362, correlation about mean = 0.2198, overlap = 1.935e+04  
steps = 64, shift = 0.521, angle = 0.419 degrees  
  
Position of W20_J4021_005_volume_map_bprime_local.mrc (#13) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998250 0.00590533 0.00034832 -0.90323251  
-0.00590377 0.99997332 -0.00430079 1.11548441  
-0.00037371 0.00429865 0.99999069 -0.31823043  
Axis 0.58794667 0.04936530 -0.80739196  
Axis point 190.18082923 131.70665579 0.00000000  
Rotation angle (degrees) 0.41901428  
Shift along axis -0.21904963  
  

> fitmap #14 inMap #1

Fit map W20_J4021_005_volume_map_sharp_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137893 points  
correlation = 0.8085, correlation about mean = 0.2734, overlap = 2.896e+04  
steps = 48, shift = 0.598, angle = 0.487 degrees  
  
Position of W20_J4021_005_volume_map_sharp_bprime_local.mrc (#14) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997911 0.00638470 0.00100265 -1.04735728  
-0.00637907 0.99996444 -0.00551663 1.34954856  
-0.00103783 0.00551011 0.99998428 -0.33308547  
Axis 0.64900636 0.12009752 -0.75124386  
Axis point 215.82672874 137.56284372 -0.00000000  
Rotation angle (degrees) 0.48673885  
Shift along axis -0.26743568  
  

> hide #!14 models

> hide #!13 models

> show #!15 models

> show #!16 models

> fitmap #15 inMap #1

Fit map W20_J4022_005_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138200 points  
correlation = 0.8381, correlation about mean = 0.222, overlap = 1.906e+04  
steps = 40, shift = 0.303, angle = 0.34 degrees  
  
Position of W20_J4022_005_volume_map_bprime_local.mrc (#15) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998447 0.00240641 0.00502780 -1.28358869  
-0.00241668 0.99999501 0.00203622 -0.22148190  
-0.00502288 -0.00204834 0.99998529 1.05482120  
Axis -0.34402829 0.84653419 -0.40623194  
Axis point 195.11366625 0.00000000 267.83446555  
Rotation angle (degrees) 0.34013109  
Shift along axis -0.17440325  
  

> fitmap #16 inMap #1

Fit map W20_J4022_005_volume_map_sharp_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138084 points  
correlation = 0.8046, correlation about mean = 0.274, overlap = 2.955e+04  
steps = 48, shift = 0.324, angle = 0.293 degrees  
  
Position of W20_J4022_005_volume_map_sharp_bprime_local.mrc (#16) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999153 0.00141184 0.00386537 -0.96250876  
-0.00142356 0.99999440 0.00302979 -0.53091994  
-0.00386107 -0.00303526 0.99998794 0.99298679  
Axis -0.59323978 0.75574456 -0.27733863  
Axis point 248.76134938 0.00000000 265.76556629  
Rotation angle (degrees) 0.29288616  
Shift along axis -0.10563498  
  

> hide #!16 models

> hide #!15 models

> show #!17 models

> fitmap #17 inMap #1

Fit map W20_J4023_003_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138098 points  
correlation = 0.8373, correlation about mean = 0.2151, overlap = 1.874e+04  
steps = 68, shift = 0.363, angle = 0.333 degrees  
  
Position of W20_J4023_003_volume_map_bprime_local.mrc (#17) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998345 0.00557936 0.00140325 -1.18658067  
-0.00557823 0.99998411 -0.00081217 0.60425107  
-0.00140776 0.00080432 0.99999869 0.20586820  
Axis 0.13912185 0.24192785 -0.96026873  
Axis point 117.12498270 207.62002695 0.00000000  
Rotation angle (degrees) 0.33286852  
Shift along axis -0.21658293  
  

> show #!18 models

> fitmap #18 inMap #1

Fit map W20_J4023_003_volume_map_sharp_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138171 points  
correlation = 0.7947, correlation about mean = 0.312, overlap = 3.526e+04  
steps = 68, shift = 0.461, angle = 0.264 degrees  
  
Position of W20_J4023_003_volume_map_sharp_bprime_local.mrc (#18) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999048 0.00393326 0.00188760 -1.06407059  
-0.00393046 0.99999117 -0.00148458 0.41525484  
-0.00189342 0.00147715 0.99999712 0.25585356  
Axis 0.32142171 0.41033635 -0.85341207  
Axis point 145.82615217 239.01637261 0.00000000  
Rotation angle (degrees) 0.26397543  
Shift along axis -0.38996975  
  

> hide #!18 models

> hide #!17 models

> show #!19 models

> fitmap #19 inMap #1

Fit map W20_J4024_005_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138193 points  
correlation = 0.8392, correlation about mean = 0.2773, overlap = 1.921e+04  
steps = 76, shift = 0.289, angle = 0.259 degrees  
  
Position of W20_J4024_005_volume_map_bprime_local.mrc (#19) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999040 0.00368324 0.00237314 -0.77269801  
-0.00368586 0.99999260 0.00110036 0.16957827  
-0.00236907 -0.00110910 0.99999658 0.39066327  
Axis -0.24448082 0.52473318 -0.81540433  
Axis point 51.36886426 212.61995395 0.00000000  
Rotation angle (degrees) 0.25890214  
Shift along axis -0.04065533  
  

> fitmap #20 inMap #1

Fit map W20_J4024_005_volume_map_sharp_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138123 points  
correlation = 0.8039, correlation about mean = 0.2975, overlap = 2.959e+04  
steps = 48, shift = 0.294, angle = 0.249 degrees  
  
Position of W20_J4024_005_volume_map_sharp_bprime_local.mrc (#20) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999177 0.00343445 0.00216100 -0.68440650  
-0.00343784 0.99999286 0.00156920 0.06668376  
-0.00215559 -0.00157662 0.99999643 0.45265088  
Axis -0.36142806 0.49593828 -0.78956633  
Axis point 30.06869516 207.44842694 0.00000000  
Rotation angle (degrees) 0.24934854  
Shift along axis -0.07696315  
  

> hide #!19 models

> show #!20 models

> hide #!20 models

> show #!21 models

> fitmap #21 inMap #1

Fit map W20_J4025_004_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138084 points  
correlation = 0.8289, correlation about mean = 0.1891, overlap = 1.832e+04  
steps = 48, shift = 0.728, angle = 0.413 degrees  
  
Position of W20_J4025_004_volume_map_bprime_local.mrc (#21) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998460 0.00544119 0.00108928 -0.83012202  
-0.00543611 0.99997458 -0.00461454 1.00696868  
-0.00111436 0.00460855 0.99998876 -0.07337997  
Axis 0.63914215 0.15270809 -0.75377553  
Axis point 193.72853355 115.34838902 0.00000000  
Rotation angle (degrees) 0.41340458  
Shift along axis -0.32148169  
  

> fitmap #22 inMap #1

Fit map W20_J4025_004_volume_map_sharp_bprime_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137654 points  
correlation = 0.7511, correlation about mean = 0.2821, overlap = 3.85e+04  
steps = 52, shift = 0.819, angle = 0.498 degrees  
  
Position of W20_J4025_004_volume_map_sharp_bprime_local.mrc (#22) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998155 0.00559478 0.00236633 -1.03081576  
-0.00557996 0.99996507 -0.00622345 1.34930492  
-0.00240107 0.00621013 0.99997783 -0.00730733  
Axis 0.71523902 0.27424352 -0.64282473  
Axis point 0.00000000 39.53456477 232.56399021  
Rotation angle (degrees) 0.49801542  
Shift along axis -0.36254420  
  

> show #!22 models

> hide #!22 models

> hide #!21 models

> show #!23 models

> show #!24 models

> fitmap #23 inMap #1

Fit map W20_J4026_004_volume_map_gammazeta_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138172 points  
correlation = 0.8607, correlation about mean = 0.3259, overlap = 2.201e+04  
steps = 52, shift = 0.541, angle = 0.494 degrees  
  
Position of W20_J4026_004_volume_map_gammazeta_local.mrc (#23) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997866 -0.00017168 -0.00653102 0.57575571  
0.00020836 0.99998421 0.00561565 -0.37594588  
0.00652995 -0.00561689 0.99996290 0.02009032  
Axis -0.65188430 -0.75799762 0.02205601  
Axis point -2.93047519 0.00000000 79.19172412  
Rotation angle (degrees) 0.49363480  
Shift along axis -0.08991691  
  

> fitmap #24 inMap #1

Fit map W20_J4026_004_volume_map_sharp_gammazeta_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138033 points  
correlation = 0.853, correlation about mean = 0.3795, overlap = 2.779e+04  
steps = 68, shift = 0.477, angle = 0.571 degrees  
  
Position of W20_J4026_004_volume_map_sharp_gammazeta_local.mrc (#24) relative
to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99996930 -0.00126227 -0.00773336 0.96231167  
0.00130980 0.99998026 0.00614469 -0.62594677  
0.00772545 -0.00615463 0.99995122 -0.10724743  
Axis -0.61739139 -0.77598860 0.12911066  
Axis point 12.56321001 0.00000000 114.62740380  
Rotation angle (degrees) 0.57071652  
Shift along axis -0.12224217  
  

> hide #!24 models

> hide #!23 models

> show #!25 models

> show #!26 models

> fitmap #25 inMap #1

Fit map W20_J4027_005_volume_map_gammazeta_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138160 points  
correlation = 0.8845, correlation about mean = 0.4248, overlap = 2.208e+04  
steps = 48, shift = 0.937, angle = 0.528 degrees  
  
Position of W20_J4027_005_volume_map_gammazeta_local.mrc (#25) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99995803 -0.00131908 0.00906657 -1.56861951  
0.00131039 0.99999868 0.00096483 0.05951128  
-0.00906783 -0.00095291 0.99995843 2.12791102  
Axis -0.10408825 0.98427482 0.14271899  
Axis point 225.62409153 0.00000000 168.02231673  
Rotation angle (degrees) 0.52781987  
Shift along axis 0.52554363  
  

> fitmap #26 inMap #1

Fit map W20_J4027_005_volume_map_sharp_gammazeta_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138211 points  
correlation = 0.8774, correlation about mean = 0.4648, overlap = 2.896e+04  
steps = 48, shift = 0.956, angle = 0.621 degrees  
  
Position of W20_J4027_005_volume_map_sharp_gammazeta_local.mrc (#26) relative
to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99994135 -0.00098967 0.01078522 -1.85651387  
0.00098601 0.99999945 0.00034465 0.18754839  
-0.01078555 -0.00033399 0.99994178 2.30481893  
Axis -0.03131444 0.99534338 0.09116443  
Axis point 208.92157622 0.00000000 171.95034602  
Rotation angle (degrees) 0.62086019  
Shift along axis 0.45492826  
  

> hide #!26 models

> hide #!25 models

> show #!27 models

> fitmap #27 inMap #1

Fit map W20_J4028_004_volume_map_gammazeta_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138218 points  
correlation = 0.8752, correlation about mean = 0.4062, overlap = 2.23e+04  
steps = 44, shift = 0.478, angle = 0.403 degrees  
  
Position of W20_J4028_004_volume_map_gammazeta_local.mrc (#27) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997775 0.00042654 -0.00665697 0.77827945  
-0.00041158 0.99999739 0.00224763 0.14049133  
0.00665791 -0.00224484 0.99997532 -0.37918036  
Axis -0.31912872 -0.94583944 -0.05953667  
Axis point 60.52816960 0.00000000 99.51494449  
Rotation angle (degrees) 0.40328886  
Shift along axis -0.35867843  
  

> fitmap #28 inMap #1

Fit map W20_J4028_004_volume_map_sharp_gammazeta_local.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137995 points  
correlation = 0.8679, correlation about mean = 0.4447, overlap = 2.897e+04  
steps = 48, shift = 0.432, angle = 0.487 degrees  
  
Position of W20_J4028_004_volume_map_sharp_gammazeta_local.mrc (#28) relative
to W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99996809 -0.00001305 -0.00798826 1.06130917  
0.00003628 0.99999577 0.00290797 -0.02300922  
0.00798819 -0.00290817 0.99996387 -0.53329988  
Axis -0.34208068 -0.93966610 0.00290175  
Axis point 67.16980128 0.00000000 117.90291440  
Rotation angle (degrees) 0.48708480  
Shift along axis -0.34297988  
  

> show #!28 models

> hide #!28 models

> show #!28 models

> hide #!28 models

> hide #!27 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body001.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body002.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body003.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J140_run_body004.mrc"

Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.00608, step 1, values float32  
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.00134, step 1, values float32  
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000955, step 1, values float32  
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000493, step 1, values float32  

> select add #29

9 models selected  

> view matrix models
> #29,-0.47366,-0.87946,-0.046912,333.91,-0.83829,0.43388,0.33018,153.37,-0.27003,0.19572,-0.94275,297.34

> ui mousemode right "translate selected models"

> view matrix models
> #29,-0.47366,-0.87946,-0.046912,340.41,-0.83829,0.43388,0.33018,139.03,-0.27003,0.19572,-0.94275,298.38

> fitmap #29 inMap #1

Multiple maps for #29  

> fitmap #29.1 inMap #1

Fit map W20_J140_run_body001.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138225 points  
correlation = 0.9233, correlation about mean = 0.7294, overlap = 874.3  
steps = 156, shift = 14.4, angle = 22 degrees  
  
Position of W20_J140_run_body001.mrc (#29.1) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95200729 0.18684598 -0.24242669 1.82192845  
-0.12799492 0.96249869 0.23919359 -9.97975402  
0.27802773 -0.19668465 0.94022111 9.66133125  
Axis -0.58247333 -0.69549428 -0.42072857  
Axis point -33.51580829 0.00000000 18.51090823  
Rotation angle (degrees) 21.97250066  
Shift along axis 1.81483897  
  

> fitmap #29.2 inMap #1

Fit map W20_J140_run_body002.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138046 points  
correlation = 0.8263, correlation about mean = 0.6371, overlap = 468.8  
steps = 280, shift = 31, angle = 21.8 degrees  
  
Position of W20_J140_run_body002.mrc (#29.2) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95172436 0.17711878 -0.25069840 4.25540621  
-0.11810903 0.96515525 0.23350719 -10.43311409  
0.28332138 -0.19262473 0.93948108 8.13777130  
Axis -0.57255681 -0.71751644 -0.39667222  
Axis point -25.70139502 0.00000000 26.08327898  
Rotation angle (degrees) 21.84708246  
Shift along axis 1.82144130  
  

> fitmap #29.3 inMap #1

Fit map W20_J140_run_body003.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137660 points  
correlation = 0.5389, correlation about mean = 0.1615, overlap = 221.3  
steps = 180, shift = 25.4, angle = 11.9 degrees  
  
Position of W20_J140_run_body003.mrc (#29.3) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98378563 0.15518997 -0.08989941 -25.87512376  
-0.14501363 0.98324752 0.11043264 11.64818978  
0.10553141 -0.09560540 0.98980944 10.88183562  
Axis -0.49859202 -0.47292359 -0.72646353  
Axis point 58.49450968 174.49109696 0.00000000  
Rotation angle (degrees) 11.92434111  
Shift along axis -0.51283023  
  

> fitmap #29.4 inMap #1

Fit map W20_J140_run_body004.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137970 points  
correlation = 0.7171, correlation about mean = 0.4553, overlap = 200.6  
steps = 192, shift = 16.7, angle = 21.7 degrees  
  
Position of W20_J140_run_body004.mrc (#29.4) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.95301433 0.19868762 -0.22866331 -0.93326951  
-0.14395018 0.96121397 0.23525740 -8.31020320  
0.26653710 -0.19128756 0.94465181 8.81821407  
Axis -0.57801628 -0.67105211 -0.46431266  
Axis point -34.90313676 0.00000000 8.20072337  
Rotation angle (degrees) 21.65230186  
Shift along axis 2.02161595  
  

> select subtract #29

Nothing selected  

> select add #29

9 models selected  

> select add #29.1

9 models selected  

> select subtract #29.1

7 models selected  

> select add #29.1

9 models selected  

> select subtract #29.1

7 models selected  

> color #29 darkgrey models

> color #29 #a9a9a993 models

> color #29 #a9a9a994 models

> select add #29

9 models selected  

> select subtract #29

Nothing selected  

> hide #!29 models

> rename #29 W20_J140_MB

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body001.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body002.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body003.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J145_run_ct8_body004.mrc"

Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.00616, step 1, values float32  
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00152, step 1, values float32  
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.000716, step 1, values float32  
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.000812, step 1, values float32  

> select add #30

9 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #30,-0.35278,-0.9274,-0.12442,348.28,-0.78005,0.21805,0.5865,134.81,-0.51679,0.30396,-0.80034,301.49

> ui mousemode right "translate selected models"

> view matrix models
> #30,-0.35278,-0.9274,-0.12442,340.27,-0.78005,0.21805,0.5865,136.72,-0.51679,0.30396,-0.80034,288.45

> fitmap #30.4 inMap #1

Fit map W20_J145_run_ct8_body004.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137951 points  
correlation = 0.7282, correlation about mean = 0.4288, overlap = 228.8  
steps = 112, shift = 11.5, angle = 9.2 degrees  
  
Position of W20_J145_run_ct8_body004.mrc (#30.4) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98788522 -0.14632868 -0.05167889 26.91126566  
0.14822194 0.98833778 0.03490982 -21.95721425  
0.04596789 -0.04214685 0.99805340 -1.50223115  
Axis -0.24099906 -0.30539579 0.92122357  
Axis point 163.78780037 168.43265871 0.00000000  
Rotation angle (degrees) 9.19930630  
Shift along axis -1.16383962  
  

> fitmap #30.3 inMap #1

Fit map W20_J145_run_ct8_body003.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137543 points  
correlation = 0.6493, correlation about mean = 0.3323, overlap = 237.6  
steps = 116, shift = 8.58, angle = 1.99 degrees  
  
Position of W20_J145_run_ct8_body003.mrc (#30.3) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99943608 -0.00513122 -0.03318412 -0.25293108  
0.00484442 0.99995027 -0.00871730 -4.33467984  
0.03322720 0.00855163 0.99941124 -5.67738477  
Axis 0.24904308 -0.95774784 0.14386320  
Axis point 184.40566041 0.00000000 -35.31005024  
Rotation angle (degrees) 1.98687515  
Shift along axis 3.27177278  
  

> fitmap #30.2 inMap #1

Fit map W20_J145_run_ct8_body002.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137963 points  
correlation = 0.8212, correlation about mean = 0.6198, overlap = 468.2  
steps = 92, shift = 7.64, angle = 3.06 degrees  
  
Position of W20_J145_run_ct8_body002.mrc (#30.2) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99870570 0.02334084 -0.04519002 -1.99430024  
-0.02260011 0.99960285 0.01683358 -2.36740438  
0.04556498 -0.01579049 0.99883657 -3.32045770  
Axis -0.30540022 -0.84957484 -0.43006196  
Axis point 34.20968149 0.00000000 -17.75195541  
Rotation angle (degrees) 3.06173952  
Shift along axis 4.04834949  
  

> fitmap #30.1 inMap #1

Fit map W20_J145_run_ct8_body001.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138203 points  
correlation = 0.9153, correlation about mean = 0.7173, overlap = 857.4  
steps = 84, shift = 6.27, angle = 2.89 degrees  
  
Position of W20_J145_run_ct8_body001.mrc (#30.1) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99917915 0.02581546 -0.03121838 -4.27539402  
-0.02486602 0.99922761 0.03042809 -4.63326697  
0.03197979 -0.02962683 0.99904932 0.16478454  
Axis -0.59553173 -0.62670160 -0.50258041  
Axis point -90.45500707 0.00000000 -32.19034476  
Rotation angle (degrees) 2.89015105  
Shift along axis 5.36699111  
  

> color #30 darkgrey models

> color #30 #a9a9a980 models

> select subtract #30

Nothing selected  

> hide #!30 models

> rename #30 W20_J145_MB

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body001.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body002.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body003.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J150_run_body004.mrc"

Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0066, step 1, values float32  
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0013, step 1, values float32  
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000798, step 1, values float32  
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000426, step 1, values float32  

> select add #31

9 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #31,0.62778,0.15918,-0.76194,138.56,0.19756,0.91423,0.35377,-64.97,0.7529,-0.37262,0.54248,29.724

> view matrix models
> #31,-0.3321,-0.94322,0.0062597,329.8,-0.75269,0.269,0.60092,127.95,-0.56848,0.19485,-0.79929,311.9

> ui mousemode right "translate selected models"

> view matrix models
> #31,-0.3321,-0.94322,0.0062597,332.22,-0.75269,0.269,0.60092,127.27,-0.56848,0.19485,-0.79929,317.96

> fitmap #31.1 inMap #1

Fit map W20_J150_run_body001.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138218 points  
correlation = 0.9172, correlation about mean = 0.7038, overlap = 893.5  
steps = 88, shift = 6.98, angle = 8.67 degrees  
  
Position of W20_J150_run_body001.mrc (#31.1) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99964242 -0.02165534 0.01568687 5.92000022  
0.01908723 0.98871756 0.14857073 -17.88200850  
-0.01872723 -0.14821819 0.98877736 29.33526708  
Axis -0.98423540 0.11412684 0.13511379  
Axis point 0.00000000 191.49090363 131.90319589  
Rotation angle (degrees) 8.67162751  
Shift along axis -3.90389179  
  

> fitmap #31.2 inMap #1

Fit map W20_J150_run_body002.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138140 points  
correlation = 0.8053, correlation about mean = 0.5992, overlap = 456.9  
steps = 116, shift = 12.3, angle = 8.44 degrees  
  
Position of W20_J150_run_body002.mrc (#31.2) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99987004 -0.01303295 0.00948916 5.64171510  
0.01150966 0.98923255 0.14589889 -15.99717561  
-0.01128848 -0.14577072 0.98925400 27.73858221  
Axis -0.99397729 0.07080790 0.08363845  
Axis point 0.00000000 183.90016756 121.07225767  
Rotation angle (degrees) 8.43680332  
Shift along axis -4.42045109  
  

> fitmap #31.3 inMap #1

Fit map W20_J150_run_body003.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137514 points  
correlation = 0.6146, correlation about mean = 0.266, overlap = 238.9  
steps = 124, shift = 9.37, angle = 6.56 degrees  
  
Position of W20_J150_run_body003.mrc (#31.3) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99927585 -0.03094085 0.02214582 5.52526341  
0.02837142 0.99372585 0.10818506 -14.70532330  
-0.02535421 -0.10747841 0.99388408 23.92950955  
Axis -0.94316639 0.20773307 0.25939184  
Axis point 0.00000000 219.38003792 144.69692071  
Rotation angle (degrees) 6.56495264  
Shift along axis -2.05890526  
  

> fitmap #31.4 inMap #1

Fit map W20_J150_run_body004.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137710 points  
correlation = 0.7262, correlation about mean = 0.4714, overlap = 200  
steps = 100, shift = 8.31, angle = 7.56 degrees  
  
Position of W20_J150_run_body004.mrc (#31.4) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99968731 -0.01039845 0.02274087 4.61807189  
0.00737128 0.99156997 0.12936254 -14.95364310  
-0.02389433 -0.12915446 0.99133656 25.99366724  
Axis -0.98187156 0.17712480 0.06749108  
Axis point 0.00000000 195.98514242 120.93339845  
Rotation angle (degrees) 7.56466213  
Shift along axis -5.42867381  
  

> color #31 darkgrey models

> color #31 #a9a9a980 models

> select subtract #31

Nothing selected  

> hide #!31 models

> rename #31 W20_J150_MB

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body001.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body002.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body003.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J155_run_ct6_body004.mrc"

Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0064, step 1, values float32  
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.00156, step 1, values float32  
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.000666, step 1, values float32  
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.000439, step 1, values float32  

> select add #32

9 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #32,-0.094929,-0.99244,0.07775,390.6,-0.44492,0.11217,0.88852,96.076,-0.89053,0.049754,-0.45221,395

> ui mousemode right "translate selected models"

> view matrix models
> #32,-0.094929,-0.99244,0.07775,372.3,-0.44492,0.11217,0.88852,92.438,-0.89053,0.049754,-0.45221,335.63

> ui mousemode right "translate selected models"

> view matrix models
> #32,-0.094929,-0.99244,0.07775,368.31,-0.44492,0.11217,0.88852,91.761,-0.89053,0.049754,-0.45221,322.87

> ui mousemode right "rotate selected models"

> view matrix models
> #32,0.24986,-0.92724,-0.27892,355.61,-0.7966,-0.36061,0.48518,310.1,-0.55046,0.10096,-0.82874,322.22

> ui mousemode right "translate selected models"

> view matrix models
> #32,0.24986,-0.92724,-0.27892,326.75,-0.7966,-0.36061,0.48518,243.97,-0.55046,0.10096,-0.82874,318.12

> ui mousemode right "rotate selected models"

> view matrix models
> #32,0.049187,-0.95013,-0.30796,371.28,-0.76011,-0.23563,0.60556,193.56,-0.64792,0.2043,-0.7338,299.66

> view matrix models
> #32,-0.38216,-0.71778,-0.58202,446.74,-0.57887,-0.30499,0.75623,147.95,-0.72032,0.62591,-0.29895,168.04

> view matrix models
> #32,-0.12174,-0.98206,-0.14398,378.68,-0.79719,0.01032,0.60364,153.76,-0.59133,0.18827,-0.78414,308.73

> ui mousemode right "translate selected models"

> view matrix models
> #32,-0.12174,-0.98206,-0.14398,339.88,-0.79719,0.01032,0.60364,183.81,-0.59133,0.18827,-0.78414,311.67

> view matrix models
> #32,-0.12174,-0.98206,-0.14398,341.73,-0.79719,0.01032,0.60364,179.24,-0.59133,0.18827,-0.78414,317.95

> fitmap #32.4 inMap #1

Fit map W20_J155_run_ct6_body004.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137851 points  
correlation = 0.7818, correlation about mean = 0.5257, overlap = 192.1  
steps = 124, shift = 4.21, angle = 14.8 degrees  
  
Position of W20_J155_run_ct6_body004.mrc (#32.4) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96755911 -0.24974155 0.03819070 46.04596253  
0.24817341 0.96782709 0.04148106 -19.98854272  
-0.04732154 -0.03065746 0.99840913 9.25104536  
Axis -0.14135691 0.16756298 0.97567457  
Axis point 102.10235956 170.64051821 0.00000000  
Rotation angle (degrees) 14.78333075  
Shift along axis -0.83224502  
  

> fitmap #32.3 inMap #1

Fit map W20_J155_run_ct6_body003.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137790 points  
correlation = 0.5288, correlation about mean = 0.2458, overlap = 222.1  
steps = 212, shift = 24.3, angle = 25.3 degrees  
  
Position of W20_J155_run_ct6_body003.mrc (#32.3) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96236345 -0.02996556 0.27010858 -46.55042113  
-0.06370212 0.94133951 0.33139398 -51.24613942  
-0.26419429 -0.33612794 0.90400187 97.79261178  
Axis -0.78009899 0.62441264 -0.03942621  
Axis point 0.00000000 234.71472833 197.05127274  
Rotation angle (degrees) 25.33083616  
Shift along axis 0.45960726  
  

> fitmap #32.2 inMap #1

Fit map W20_J155_run_ct6_body002.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138167 points  
correlation = 0.8427, correlation about mean = 0.6574, overlap = 508.2  
steps = 200, shift = 28.2, angle = 13.9 degrees  
  
Position of W20_J155_run_ct6_body002.mrc (#32.2) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97079416 -0.23981830 0.00677387 48.62036376  
0.23979745 0.97081570 0.00375114 -13.12837058  
-0.00747577 -0.00201723 0.99997002 1.33700507  
Axis -0.01202088 0.02969530 0.99948671  
Axis point 78.30820657 193.21986153 0.00000000  
Rotation angle (degrees) 13.88246944  
Shift along axis 0.36200848  
  

> fitmap #32.1 inMap #1

Fit map W20_J155_run_ct6_body001.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138158 points  
correlation = 0.9152, correlation about mean = 0.7176, overlap = 887.9  
steps = 240, shift = 17.9, angle = 14.3 degrees  
  
Position of W20_J155_run_ct6_body001.mrc (#32.1) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96918769 -0.24592134 0.01406818 48.78106404  
0.24563656 0.96916974 0.01930526 -16.53168875  
-0.01838203 -0.01525477 0.99971466 4.87447888  
Axis -0.06998243 0.06571014 0.99538165  
Axis point 90.87557164 187.07445802 0.00000000  
Rotation angle (degrees) 14.29528730  
Shift along axis 0.35184982  
  

> select add #32.3

9 models selected  

> select subtract #32

Nothing selected  

> select subtract #32.3

Nothing selected  

> select add #32.3

2 models selected  

> view matrix models
> #32.3,0.96236,-0.029966,0.27011,-49.146,-0.063702,0.94134,0.33139,-16.537,-0.26419,-0.33613,0.904,117.55

> fitmap #32.3 inMap #1

Fit map W20_J155_run_ct6_body003.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137790 points  
correlation = 0.5773, correlation about mean = 0.2332, overlap = 255.7  
steps = 220, shift = 22.6, angle = 31.2 degrees  
  
Position of W20_J155_run_ct6_body003.mrc (#32.3) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93701301 -0.34494790 0.05493240 55.45886688  
0.34457856 0.93861493 0.01635939 -26.98464957  
-0.05720351 0.00359956 0.99835605 3.33562233  
Axis -0.01826220 0.16049183 0.98686821  
Axis point 102.63951914 141.92416208 0.00000000  
Rotation angle (degrees) 20.44761418  
Shift along axis -2.05179723  
  

> select subtract #32.3

Nothing selected  

> color #32 #929292ff models

> color #32 #9292927d models

> hide #!32 models

> rename #32 W20_J155_MB

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body001.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body002.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body003.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/relionMB/W20_J160_run_ct6_body004.mrc"

Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.00725, step 1, values float32  
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.00154, step 1, values float32  
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.000864, step 1, values float32  
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.000379, step 1, values float32  

> select add #33

9 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #33,0.31873,-0.82608,0.46476,171.28,-0.72157,0.10647,0.6841,150.82,-0.6146,-0.5534,-0.56214,456.98

> view matrix models
> #33,-0.036679,-0.99898,-0.026385,337.23,-0.84584,0.016974,0.53317,211.08,-0.53218,0.041873,-0.8456,383.69

> ui mousemode right "translate selected models"

> view matrix models
> #33,-0.036679,-0.99898,-0.026385,334.88,-0.84584,0.016974,0.53317,195.64,-0.53218,0.041873,-0.8456,333.69

> view matrix models
> #33,-0.036679,-0.99898,-0.026385,313.34,-0.84584,0.016974,0.53317,188.83,-0.53218,0.041873,-0.8456,328.42

> view matrix models
> #33,-0.036679,-0.99898,-0.026385,311.41,-0.84584,0.016974,0.53317,189.7,-0.53218,0.041873,-0.8456,344.34

> ui mousemode right "rotate selected models"

> view matrix models
> #33,-0.35879,-0.93341,-0.0038469,340.33,-0.80584,0.30767,0.50593,135.86,-0.47106,0.18462,-0.86256,313.27

> ui mousemode right "translate selected models"

> view matrix models
> #33,-0.35879,-0.93341,-0.0038469,338.34,-0.80584,0.30767,0.50593,141.61,-0.47106,0.18462,-0.86256,318.7

> fitmap #33.3 inMap #1

Fit map W20_J160_run_ct6_body003.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137937 points  
correlation = 0.5867, correlation about mean = 0.2346, overlap = 250.3  
steps = 140, shift = 11.6, angle = 7.35 degrees  
  
Position of W20_J160_run_ct6_body003.mrc (#33.3) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99303756 0.05988139 0.10144267 -23.49545369  
-0.06488899 0.99679433 0.04680249 14.70011589  
-0.09831488 -0.05305914 0.99373986 28.54412294  
Axis -0.39036137 0.78085672 -0.48773024  
Axis point 309.26276930 0.00000000 226.94693512  
Rotation angle (degrees) 7.34879054  
Shift along axis 6.72856998  
  

> fitmap #33.2 inMap #1

Fit map W20_J160_run_ct6_body002.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137991 points  
correlation = 0.819, correlation about mean = 0.6067, overlap = 480.4  
steps = 144, shift = 18.2, angle = 13.8 degrees  
  
Position of W20_J160_run_ct6_body002.mrc (#33.2) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99771963 -0.01489642 -0.06583042 17.27645423  
0.02956838 0.97323369 0.22790766 -26.83710836  
0.06067337 -0.22933444 0.97145481 35.68296509  
Axis -0.95958803 -0.26548631 0.09331575  
Axis point 0.00000000 140.48687556 141.38690851  
Rotation angle (degrees) 13.78322772  
Shift along axis -6.12361124  
  

> fitmap #33.1 inMap #1

Fit map W20_J160_run_ct6_body001.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 138219 points  
correlation = 0.9149, correlation about mean = 0.7061, overlap = 905.5  
steps = 240, shift = 9.92, angle = 13.4 degrees  
  
Position of W20_J160_run_ct6_body001.mrc (#33.1) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99744755 -0.02103927 -0.06823292 18.77482829  
0.03561801 0.97482901 0.22009032 -27.49182319  
0.06188489 -0.22195888 0.97309019 34.85093721  
Axis -0.95213476 -0.28026222 0.12203477  
Axis point 0.00000000 142.23926756 148.71521434  
Rotation angle (degrees) 13.42285005  
Shift along axis -5.91822131  
  

> fitmap #33.4 inMap #1

Fit map W20_J160_run_ct6_body004.mrc in map
W20_J3623_consensus_structure_sharp.mrc using 137797 points  
correlation = 0.7345, correlation about mean = 0.436, overlap = 185.3  
steps = 144, shift = 10.1, angle = 13 degrees  
  
Position of W20_J160_run_ct6_body004.mrc (#33.4) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99800988 0.00249027 -0.06300862 14.90861204  
0.01124609 0.97617108 0.21671073 -24.80457915  
0.06204686 -0.21698805 0.97420038 33.68609528  
Axis -0.96067232 -0.27700640 0.01939474  
Axis point 0.00000000 139.38706533 138.47533972  
Rotation angle (degrees) 13.04561440  
Shift along axis -6.79793059  
  

> select subtract #33

Nothing selected  

> color #33 #929292ff models

> color #33 #92929280 models

> hide #!33 models

> rename #33 W20_J160_MB

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

——— End of log from Tue Jul 1 13:02:54 2025 ———

opened ChimeraX session  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopA-F8WHL2.pdb"

CopA-F8WHL2.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit α (F8WHL2) [more
info...]  
  
Chain information for CopA-F8WHL2.pdb #34  
---  
Chain | Description | UniProt  
A | coatomer subunit α | F8WHL2_MOUSE 1-1233  
  
Computing secondary structure  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopB_ Q9JIF7.pdb"

CopB_ Q9JIF7.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit β (Q9JIF7) [more
info...]  
  
Chain information for CopB_ Q9JIF7.pdb #35  
---  
Chain | Description | UniProt  
A | coatomer subunit β | COPB_MOUSE 1-953  
  
Computing secondary structure  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopBprime_O55029.pdb"

CopBprime_O55029.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit β' (O55029) [more
info...]  
  
Chain information for CopBprime_O55029.pdb #36  
---  
Chain | Description | UniProt  
A | coatomer subunit β' | COPB2_MOUSE 1-905  
  
Computing secondary structure  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopD_full_Q5XJY5.pdb"

CopD_full_Q5XJY5.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit δ (Q5XJY5) [more
info...]  
  
Chain information for CopD_full_Q5XJY5.pdb #37  
---  
Chain | Description | UniProt  
A | coatomer subunit δ | COPD_MOUSE 1-511  
  
Computing secondary structure  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopG1_ Q9QZE5.pdb"

CopG1_ Q9QZE5.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
info...]  
  
Chain information for CopG1_ Q9QZE5.pdb #38  
---  
Chain | Description | UniProt  
A | coatomer subunit γ-1 | COPG1_MOUSE 1-874  
  
Computing secondary structure  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopG1_ Q9QZE5.pdb"

CopG1_ Q9QZE5.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
info...]  
  
Chain information for CopG1_ Q9QZE5.pdb #39  
---  
Chain | Description | UniProt  
A | coatomer subunit γ-1 | COPG1_MOUSE 1-874  
  
Computing secondary structure  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopZ1_P61924.pdb"

CopZ1_P61924.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit ζ-1 (P61924) [more
info...]  
  
Chain information for CopZ1_P61924.pdb #40  
---  
Chain | Description | UniProt  
A | coatomer subunit ζ-1 | COPZ1_MOUSE 1-177  
  
Computing secondary structure  

> hide #40 models

> hide #39 models

> hide #38 models

> hide #37 models

> hide #36 models

> hide #35 models

> select add #34

9810 atoms, 10032 bonds, 1233 residues, 1 model selected  

> color list

28 custom colors: alphav1

, alphav2

, alphav3

, arf1v1

, arf1v2

, arf1v3

, betapv1

, betapv2

, betapv3

, betav1

, betav2

, betav3

, deltav1

, deltav2

, deltav3

, epsilonv1

, epsilonv3

, gammav1

, gammav2

, gammav3

, label_purple

, label_purple_v3

, label_red

, label_red_v3

, lable_purple_v4

, zetav1

, zetav2

, and zetav3

.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel navy

> select subtract #34

Nothing selected  

> hide #34 models

> show #35 models

> select add #35

7501 atoms, 7619 bonds, 953 residues, 1 model selected  

> color sel betav1

> select subtract #35

Nothing selected  

> hide #35 models

> show #36 models

> select add #36

7214 atoms, 7373 bonds, 905 residues, 1 model selected  

> color sel betapv2

> color sel betapv3

> select subtract #36

Nothing selected  

> hide #36 models

> show #37 models

> select add #37

4014 atoms, 4083 bonds, 511 residues, 1 model selected  

> color sel deltav3

> select subtract #37

Nothing selected  

> hide #37 models

> show #38 models

> select add #38

6830 atoms, 6947 bonds, 874 residues, 1 model selected  

> close #39

> close #40

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopZ1_P61924.pdb"

CopZ1_P61924.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit ζ-1 (P61924) [more
info...]  
  
Chain information for CopZ1_P61924.pdb #39  
---  
Chain | Description | UniProt  
A | coatomer subunit ζ-1 | COPZ1_MOUSE 1-177  
  
Computing secondary structure  

> hide #39 models

> color sel gammav3

> select subtract #38

Nothing selected  

> hide #38 models

> show #39 models

> select add #39

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> zetav3

Unknown command: zetav3  

> color sel zetav3

> select subtract #39

Nothing selected  

> hide #39 models

> show #34 models

> select add #34

9810 atoms, 10032 bonds, 1233 residues, 1 model selected  

> view matrix models #34,1,0,0,39.828,0,1,0,139.02,0,0,1,198.43

> ui mousemode right "rotate selected models"

> view matrix models
> #34,0.99004,0.0096002,0.14042,38.534,-0.012281,0.99976,0.018237,138.66,-0.14022,-0.01978,0.98992,196.08

> view matrix models
> #34,0.13783,-0.38457,0.91275,20.074,-0.096945,0.91188,0.39884,134.94,-0.9857,-0.14346,0.088401,188.13

> view matrix models
> #34,-0.34037,-0.83282,0.43653,18.135,0.30375,0.34197,0.88926,142.89,-0.88988,0.43527,0.13658,185.25

> ui mousemode right "translate selected models"

> view matrix models
> #34,-0.34037,-0.83282,0.43653,139.16,0.30375,0.34197,0.88926,104.42,-0.88988,0.43527,0.13658,153.4

> view matrix models
> #34,-0.34037,-0.83282,0.43653,161.88,0.30375,0.34197,0.88926,148.44,-0.88988,0.43527,0.13658,135.72

> ui mousemode right "rotate selected models"

> view matrix models
> #34,-0.64868,-0.43267,-0.62611,161.12,0.47729,-0.87206,0.10814,166.41,-0.59279,-0.22869,0.7722,141.4

> ui mousemode right "translate selected models"

> view matrix models
> #34,-0.64868,-0.43267,-0.62611,149.78,0.47729,-0.87206,0.10814,138.8,-0.59279,-0.22869,0.7722,155.26

> fitmap #34 inMap #1

Fit molecule CopA-F8WHL2.pdb (#34) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 9810 atoms  
average map value = 0.1956, steps = 172  
shifted from previous position = 12.4  
rotated from previous position = 16.7 degrees  
atoms outside contour = 6664, contour level = 0.26383  
  
Position of CopA-F8WHL2.pdb (#34) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.40275740 -0.50265546 -0.76493398 155.53344658  
0.55537393 -0.79849851 0.23229283 137.87047167  
-0.72756189 -0.33126673 0.60076291 143.99545516  
Axis -0.46989046 -0.03116049 0.88217458  
Axis point 89.79461102 105.24732460 0.00000000  
Rotation angle (degrees) 143.15364698  
Shift along axis 49.64933605  
  

> view matrix models
> #34,-0.40276,-0.50266,-0.76493,152.08,0.55537,-0.7985,0.23229,129.79,-0.72756,-0.33127,0.60076,131.15

> fitmap #34 inMap #1

Fit molecule CopA-F8WHL2.pdb (#34) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 9810 atoms  
average map value = 0.3026, steps = 204  
shifted from previous position = 8.55  
rotated from previous position = 12.6 degrees  
atoms outside contour = 4835, contour level = 0.26383  
  
Position of CopA-F8WHL2.pdb (#34) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.54728967 -0.56189790 -0.62027800 158.57511981  
0.58976792 -0.78477262 0.19054069 127.65605082  
-0.59384159 -0.26153911 0.76088730 134.18075471  
Axis -0.36531666 -0.02136273 0.93063815  
Axis point 81.60160811 99.25852793 0.00000000  
Rotation angle (degrees) 141.77504660  
Shift along axis 64.21651520  
  

> select subtract #34

Nothing selected  

> hide #34 models

> show #35 models

> select add #35

7501 atoms, 7619 bonds, 953 residues, 1 model selected  

> view matrix models #35,1,0,0,116.88,0,1,0,-7.2403,0,0,1,111.96

> view matrix models #35,1,0,0,112.47,0,1,0,89.143,0,0,1,196.06

> ui mousemode right "rotate selected models"

> view matrix models
> #35,0.0065824,0.90646,-0.42225,117.47,0.83324,-0.23843,-0.49886,91.055,-0.55287,-0.34855,-0.75686,209.75

> ui mousemode right "translate selected models"

> view matrix models
> #35,0.0065824,0.90646,-0.42225,96.987,0.83324,-0.23843,-0.49886,131.53,-0.55287,-0.34855,-0.75686,188.84

> view matrix models
> #35,0.0065824,0.90646,-0.42225,132.29,0.83324,-0.23843,-0.49886,123.6,-0.55287,-0.34855,-0.75686,174.35

> view matrix models
> #35,0.0065824,0.90646,-0.42225,129.73,0.83324,-0.23843,-0.49886,153.17,-0.55287,-0.34855,-0.75686,162.06

> fitmap #35 inMap #1

Fit molecule CopB_ Q9JIF7.pdb (#35) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 7501 atoms  
average map value = 0.272, steps = 140  
shifted from previous position = 13  
rotated from previous position = 19.4 degrees  
atoms outside contour = 4336, contour level = 0.26383  
  
Position of CopB_ Q9JIF7.pdb (#35) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.29878946 0.85180997 -0.43028434 135.66407916  
0.69839777 -0.50244520 -0.50969537 144.97471611  
-0.65035790 -0.14821802 -0.74502752 155.00132184  
Axis 0.80301824 0.48889117 -0.34080365  
Axis point 0.00000000 17.11569470 112.17244297  
Rotation angle (degrees) 166.99275965  
Shift along axis 126.99257230  
  

> select subtract #35

Nothing selected  

> hide #35 models

> show #36 models

> select add #36

7214 atoms, 7373 bonds, 905 residues, 1 model selected  

> view matrix models #36,1,0,0,158.6,0,1,0,131.6,0,0,1,186.36

> view matrix models #36,1,0,0,112.24,0,1,0,235.54,0,0,1,195.51

> ui mousemode right "rotate selected models"

> view matrix models
> #36,0.60674,-0.015574,0.79475,88.102,0.72366,0.42451,-0.54415,257.75,-0.3289,0.90529,0.26884,209.07

> ui mousemode right "translate selected models"

> view matrix models
> #36,0.60674,-0.015574,0.79475,110.55,0.72366,0.42451,-0.54415,182.27,-0.3289,0.90529,0.26884,183.11

> view matrix models
> #36,0.60674,-0.015574,0.79475,107.23,0.72366,0.42451,-0.54415,189.41,-0.3289,0.90529,0.26884,154.84

> view matrix models
> #36,0.60674,-0.015574,0.79475,127.45,0.72366,0.42451,-0.54415,196.73,-0.3289,0.90529,0.26884,180.58

> fitmap #36 inMap #1

Fit molecule CopBprime_O55029.pdb (#36) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 7214 atoms  
average map value = 0.2113, steps = 200  
shifted from previous position = 4.95  
rotated from previous position = 18 degrees  
atoms outside contour = 5449, contour level = 0.26383  
  
Position of CopBprime_O55029.pdb (#36) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.50276875 0.12737660 0.85498467 126.31561890  
0.61912593 0.63718187 -0.45900148 191.39912628  
-0.60324678 0.76011477 0.24149298 177.83802946  
Axis 0.62095632 0.74274954 0.25047230  
Axis point 74.13696267 0.00000000 87.94186273  
Rotation angle (degrees) 79.00508960  
Shift along axis 265.14159471  
  

> select subtract #36

Nothing selected  

> hide #36 models

> show #37 models

> select add #37

4014 atoms, 4083 bonds, 511 residues, 1 model selected  

> view matrix models #37,1,0,0,30.593,0,1,0,199.33,0,0,1,198.85

> view matrix models #37,1,0,0,157.99,0,1,0,204.81,0,0,1,141.3

> ui mousemode right "rotate selected models"

> view matrix models
> #37,0.43622,0.67922,-0.59023,141.13,-0.78114,-0.039782,-0.62309,191.16,-0.44669,0.73286,0.51321,126.99

> ui mousemode right "translate selected models"

> view matrix models
> #37,0.43622,0.67922,-0.59023,150.33,-0.78114,-0.039782,-0.62309,186.91,-0.44669,0.73286,0.51321,121.12

> view matrix models
> #37,0.43622,0.67922,-0.59023,147.14,-0.78114,-0.039782,-0.62309,187.14,-0.44669,0.73286,0.51321,128.48

> fitmap #37 inMap #1

Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 4014 atoms  
average map value = 0.1388, steps = 96  
shifted from previous position = 7.92  
rotated from previous position = 10.6 degrees  
atoms outside contour = 3125, contour level = 0.26383  
  
Position of CopD_full_Q5XJY5.pdb (#37) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.41505472 0.79215751 -0.44745509 152.46783193  
-0.75869096 0.02993242 -0.65076269 180.94994695  
-0.50211314 0.60958226 0.61342633 132.05032423  
Axis 0.63044142 0.02734069 -0.77575518  
Axis point 250.00196774 -8.95488713 0.00000000  
Rotation angle (degrees) 88.32633929  
Shift along axis -1.36938916  
  

> view matrix models
> #37,0.41505,0.79216,-0.44746,143.76,-0.75869,0.029932,-0.65076,186.11,-0.50211,0.60958,0.61343,122.85

> view matrix models
> #37,0.41505,0.79216,-0.44746,143.43,-0.75869,0.029932,-0.65076,185.75,-0.50211,0.60958,0.61343,122.85

> view matrix models
> #37,0.41505,0.79216,-0.44746,142.4,-0.75869,0.029932,-0.65076,174.97,-0.50211,0.60958,0.61343,117.62

> fitmap #37 inMap #1

Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 4014 atoms  
average map value = 0.1655, steps = 240  
shifted from previous position = 19.2  
rotated from previous position = 30 degrees  
atoms outside contour = 2918, contour level = 0.26383  
  
Position of CopD_full_Q5XJY5.pdb (#37) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54325309 0.50781797 -0.66857834 156.40844261  
-0.83919938 0.30481815 -0.45036685 164.83901629  
-0.02490957 0.80573371 0.59175392 110.35264351  
Axis 0.64381104 -0.32991074 -0.69041020  
Axis point 270.01565892 -103.01400891 0.00000000  
Rotation angle (degrees) 77.29610173  
Shift along axis -29.87327013  
  

> view matrix models
> #37,0.54325,0.50782,-0.66858,154.11,-0.8392,0.30482,-0.45037,160.13,-0.02491,0.80573,0.59175,113.09

> view matrix models
> #37,0.54325,0.50782,-0.66858,152.8,-0.8392,0.30482,-0.45037,160.99,-0.02491,0.80573,0.59175,116.7

> fitmap #37 inMap #1

Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 4014 atoms  
average map value = 0.1527, steps = 200  
shifted from previous position = 8.47  
rotated from previous position = 9.78 degrees  
atoms outside contour = 3000, contour level = 0.26383  
  
Position of CopD_full_Q5XJY5.pdb (#37) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52381084 0.45458159 -0.72040113 159.66823341  
-0.84399300 0.16247112 -0.51115453 164.46346911  
-0.11531706 0.87576179 0.46876781 118.49109089  
Axis 0.69555148 -0.30345531 -0.65124728  
Axis point 0.00000000 33.10752297 257.99354223  
Rotation angle (degrees) 85.55368957  
Shift along axis -16.01683616  
  

> select subtract #37

Nothing selected  

> hide #37 models

> show #38 models

> select add #38

6830 atoms, 6947 bonds, 874 residues, 1 model selected  

> view matrix models #38,1,0,0,4.9195,0,1,0,158.21,0,0,1,93.306

> view matrix models #38,1,0,0,20.598,0,1,0,103.1,0,0,1,122.07

> view matrix models #38,1,0,0,72.888,0,1,0,68.344,0,0,1,130.87

> view matrix models #38,1,0,0,89.688,0,1,0,109.93,0,0,1,127.2

> ui mousemode right "rotate selected models"

> view matrix models
> #38,-0.10567,0.8283,0.55022,86.046,-0.72387,0.3153,-0.61367,108.49,-0.68179,-0.46314,0.56627,125.7

> ui mousemode right "translate selected models"

> view matrix models
> #38,-0.10567,0.8283,0.55022,94.304,-0.72387,0.3153,-0.61367,138.65,-0.68179,-0.46314,0.56627,138.14

> view matrix models
> #38,-0.10567,0.8283,0.55022,112.86,-0.72387,0.3153,-0.61367,126.46,-0.68179,-0.46314,0.56627,130.13

> fitmap #38 inMap #1

Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 6830 atoms  
average map value = 0.2013, steps = 104  
shifted from previous position = 5.21  
rotated from previous position = 10.3 degrees  
atoms outside contour = 4944, contour level = 0.26383  
  
Position of CopG1_ Q9QZE5.pdb (#38) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.18152050 0.89700589 0.40302697 113.56564500  
-0.70329404 0.16803702 -0.69075398 122.94853762  
-0.68733384 -0.40883247 0.60035673 126.40848670  
Axis 0.14406783 0.55719735 -0.81778700  
Axis point 133.98876902 46.90995141 0.00000000  
Rotation angle (degrees) 101.92103286  
Shift along axis -18.50746083  
  

> select subtract #38

Nothing selected  

> hide #38 models

> show #39 models

> select add #39

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> view matrix models #39,1,0,0,9.0898,0,1,0,160.45,0,0,1,-9.3444

> view matrix models #39,1,0,0,60.276,0,1,0,127.59,0,0,1,121.27

> view matrix models #39,1,0,0,127.7,0,1,0,116.45,0,0,1,94.356

> view matrix models #39,1,0,0,126.09,0,1,0,140.04,0,0,1,103.22

> ui mousemode right "rotate selected models"

> view matrix models
> #39,0.77404,0.11317,-0.62294,121.61,-0.58601,0.50055,-0.63722,130.26,0.2397,0.85828,0.45376,105.69

> fitmap #39 inMap #1

Fit molecule CopZ1_P61924.pdb (#39) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 1420 atoms  
average map value = 0.2019, steps = 236  
shifted from previous position = 4.91  
rotated from previous position = 38.4 degrees  
atoms outside contour = 1084, contour level = 0.26383  
  
Position of CopZ1_P61924.pdb (#39) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.67082708 0.40413817 -0.62182263 120.91871935  
-0.65153203 -0.07936382 -0.75445836 130.14553587  
-0.35425563 0.91124845 0.21006956 98.85805425  
Axis 0.83698462 -0.13444710 -0.53045332  
Axis point 0.00000000 12.35504647 160.39862757  
Rotation angle (degrees) 95.69503877  
Shift along axis 31.26983397  
  

> select subtract #39

Nothing selected  

> hide #39 models

> show #39 models

> show #38 models

> show #37 models

> show #36 models

> show #35 models

> show #34 models

> hide #!1 models

> show #!3 models

> fitmap #36 inMap #3

Fit molecule CopBprime_O55029.pdb (#36) to map
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
using 7214 atoms  
average map value = 0.2322, steps = 64  
shifted from previous position = 2.88  
rotated from previous position = 4.24 degrees  
atoms outside contour = 4591, contour level = 0.26875  
  
Position of CopBprime_O55029.pdb (#36) relative to
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.39263805 -0.91469425 -0.09575906 92.65990042  
-0.55910845 0.32006970 -0.76482228 179.90077864  
0.73022811 -0.24675864 -0.63708483 150.47739175  
Axis 0.49918086 -0.79588095 0.34262513  
Axis point 73.56777391 0.00000000 134.22819381  
Rotation angle (degrees) 148.74058258  
Shift along axis -45.36821860  
  

> fitmap #35 inMap #3

Fit molecule CopB_ Q9JIF7.pdb (#35) to map
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
using 7501 atoms  
average map value = 0.2689, steps = 112  
shifted from previous position = 7.58  
rotated from previous position = 7.06 degrees  
atoms outside contour = 3837, contour level = 0.26875  
  
Position of CopB_ Q9JIF7.pdb (#35) relative to
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.23385104 0.28135848 0.93067238 134.35318178  
-0.41876188 -0.89302545 0.16475441 150.63397364  
0.87746918 -0.35120213 0.32665714 138.57787474  
Axis -0.59215049 0.06105999 -0.80351072  
Axis point 39.18867412 76.76513978 0.00000000  
Rotation angle (degrees) 154.17248796  
Shift along axis -181.70840106  
  

> fitmap #34 inMap #3

Fit molecule CopA-F8WHL2.pdb (#34) to map
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
using 9810 atoms  
average map value = 0.2333, steps = 88  
shifted from previous position = 0.574  
rotated from previous position = 1.73 degrees  
atoms outside contour = 5294, contour level = 0.26875  
  
Position of CopA-F8WHL2.pdb (#34) relative to
W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.01921606 0.93572095 -0.35221737 156.63147150  
0.36634751 0.32119202 0.87328416 124.11551889  
0.93027967 -0.14581504 -0.33662699 137.77469414  
Axis -0.58763841 -0.73952029 -0.32831515  
Axis point 4.51722837 0.00000000 49.95590579  
Rotation angle (degrees) 119.87500102  
Shift along axis -229.06213308  
  

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> fitmap #38 inMap #9

Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
(#9) using 6830 atoms  
average map value = 0.2056, steps = 112  
shifted from previous position = 3.87  
rotated from previous position = 8.6 degrees  
atoms outside contour = 4655, contour level = 0.28232  
  
Position of CopG1_ Q9QZE5.pdb (#38) relative to
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
(#9) coordinates:  
Matrix rotation and translation  
0.97147165 -0.22568138 0.07287489 181.98815327  
-0.21631778 -0.96919397 -0.11776953 160.81365369  
0.09720830 0.09864563 -0.99036336 147.52870008  
Axis 0.99282083 -0.11163133 0.04295621  
Axis point 0.00000000 86.77702657 74.77347983  
Rotation angle (degrees) 173.74290119  
Shift along axis 169.06706116  
  

> hide #!9 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!23 models

> fitmap #38 inMap #23

Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
W20_J4026_004_volume_map_gammazeta_local.mrc (#23) using 6830 atoms  
average map value = 0.1938, steps = 88  
shifted from previous position = 1.48  
rotated from previous position = 1.93 degrees  
atoms outside contour = 4539, contour level = 0.26014  
  
Position of CopG1_ Q9QZE5.pdb (#38) relative to
W20_J4026_004_volume_map_gammazeta_local.mrc (#23) coordinates:  
Matrix rotation and translation  
-0.15863519 0.95166183 0.26301070 116.52908933  
-0.70798986 0.07602756 -0.70211834 119.07331926  
-0.68817529 -0.29758959 0.66170629 125.26733072  
Axis 0.20689796 0.48648815 -0.84883597  
Axis point 135.80061352 37.60568602 0.00000000  
Rotation angle (degrees) 102.14876416  
Shift along axis -24.29402645  
  

> hide #!23 models

> show #!25 models

> fitmap #38 inMap #23

Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
W20_J4026_004_volume_map_gammazeta_local.mrc (#23) using 6830 atoms  
average map value = 0.1938, steps = 48  
shifted from previous position = 0.0265  
rotated from previous position = 0.0358 degrees  
atoms outside contour = 4543, contour level = 0.26014  
  
Position of CopG1_ Q9QZE5.pdb (#38) relative to
W20_J4026_004_volume_map_gammazeta_local.mrc (#23) coordinates:  
Matrix rotation and translation  
-0.15917554 0.95152929 0.26316374 116.52898909  
-0.70811196 0.07570421 -0.70203014 119.09089645  
-0.68792485 -0.29809542 0.66173902 125.28763210  
Axis 0.20661307 0.48648289 -0.84890838  
Axis point 135.76856788 37.64517816 0.00000000  
Rotation angle (degrees) 102.17311623  
Shift along axis -24.34562541  
  

> fitmap #38 inMap #25

Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6830 atoms  
average map value = 0.2208, steps = 312  
shifted from previous position = 9.89  
rotated from previous position = 43.3 degrees  
atoms outside contour = 4003, contour level = 0.2532  
  
Position of CopG1_ Q9QZE5.pdb (#38) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.51349164 0.78944189 0.33631509 107.60498851  
-0.18358145 0.28179025 -0.94174949 122.78040261  
-0.83822681 -0.54532170 0.00022995 120.22835474  
Axis 0.25155556 0.74531240 -0.61743762  
Axis point 81.37402006 0.00000000 79.41692880  
Rotation angle (degrees) 128.00539846  
Shift along axis 44.34488087  
  

> hide #!25 models

> show #!25 models

> color #25 #929292ff models

> color #25 #92929297 models

> select add #39

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> view matrix models
> #39,0.049821,0.95099,-0.30519,123.19,-0.98555,-0.0027194,-0.16936,132.83,-0.16189,0.30922,0.93711,101.07

> ui mousemode right "translate selected models"

> view matrix models
> #39,0.049821,0.95099,-0.30519,120.81,-0.98555,-0.0027194,-0.16936,149.13,-0.16189,0.30922,0.93711,88.072

> view matrix models
> #39,0.049821,0.95099,-0.30519,127.16,-0.98555,-0.0027194,-0.16936,146.48,-0.16189,0.30922,0.93711,93.373

> fitmap #39 inMap #25

Fit molecule CopZ1_P61924.pdb (#39) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms  
average map value = 0.2155, steps = 132  
shifted from previous position = 12.7  
rotated from previous position = 24.5 degrees  
atoms outside contour = 816, contour level = 0.2532  
  
Position of CopZ1_P61924.pdb (#39) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.02172282 0.87569029 -0.48238434 117.17569269  
-0.85704432 -0.26475204 -0.44201968 143.50099331  
-0.51478457 0.40382284 0.75625654 98.49893470  
Axis 0.43861563 0.01680130 -0.89851770  
Axis point 143.73837501 16.52006781 0.00000000  
Rotation angle (degrees) 105.37343878  
Shift along axis -34.69694324  
  

> select subtract #39

Nothing selected  

> hide #39 models

> hide #38 models

> hide #37 models

> hide #36 models

> hide #35 models

> show #35 models

> hide #35 models

> hide #34 models

> show #34 models

> show #35 models

> show #36 models

> show #37 models

> show #38 models

> show #39 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_2025_01_17_alpha1_330gamma1_330zeta/fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif"

Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif #40  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  

> select add #40

6676 atoms, 6817 bonds, 837 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #40 to #34

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CopA-F8WHL2.pdb, chain A (#34) with
fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain B (#40), sequence
alignment score = 1723  
RMSD between 297 pruned atom pairs is 0.381 angstroms; (across all 330 pairs:
4.425)  
  

> select subtract #40

Nothing selected  

> fitmap #40 inMap #25

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6676 atoms  
average map value = 0.2327, steps = 120  
shifted from previous position = 12.5  
rotated from previous position = 19.1 degrees  
atoms outside contour = 3778, contour level = 0.2532  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40)
relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.54165871 0.66183244 -0.51825058 133.50428914  
0.57871718 -0.74075578 -0.34112650 139.20476253  
-0.60966570 -0.11514637 -0.78425063 100.42690475  
Axis 0.87742311 0.35494156 -0.32271532  
Axis point 0.00000000 37.30416243 78.13952669  
Rotation angle (degrees) 172.60119629  
Shift along axis 134.14000391  
  

> ui tool show Matchmaker

> matchmaker #39 to #40

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain C (#40)
with CopZ1_P61924.pdb, chain A (#39), sequence alignment score = 863.4  
RMSD between 141 pruned atom pairs is 0.407 angstroms; (across all 177 pairs:
16.666)  
  

> hide #40 models

> fitmap #39 inMap #25

Fit molecule CopZ1_P61924.pdb (#39) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms  
average map value = 0.237, steps = 448  
shifted from previous position = 13.1  
rotated from previous position = 65.5 degrees  
atoms outside contour = 774, contour level = 0.2532  
  
Position of CopZ1_P61924.pdb (#39) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.40316931 0.69456576 0.59584639 114.25318729  
-0.23944244 -0.54836159 0.80122836 139.81166245  
0.88324506 -0.46570160 -0.05477404 99.19539890  
Axis -0.79181872 -0.17962133 -0.58374591  
Axis point 0.00000000 56.29130506 -26.82207038  
Rotation angle (degrees) 126.86869176  
Shift along axis -173.48587819  
  

> undo

> hide #39 models

> hide #38 models

> hide #37 models

> hide #36 models

> hide #35 models

> hide #34 models

> hide #!25 models

> ui mousemode right select

Drag select of 102 residues  

> select up

1089 atoms, 1111 bonds, 132 residues, 1 model selected  

> select up

2689 atoms, 2767 bonds, 330 residues, 1 model selected  

> delete sel

> fitmap #40 inMap #25

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3987 atoms  
average map value = 0.2376, steps = 148  
shifted from previous position = 8.47  
rotated from previous position = 22.7 degrees  
atoms outside contour = 2154, contour level = 0.2532  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#40)
relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.25729822 0.88581488 -0.38617305 122.95584280  
0.78223190 -0.42556216 -0.45498364 149.35405458  
-0.56737191 -0.18501039 -0.80240904 100.43354571  
Axis 0.79114243 0.53099377 -0.30354451  
Axis point 0.00000000 25.55099714 77.70315234  
Rotation angle (degrees) 170.17599112  
Shift along axis 146.09560633  
  

> show #!25 models

> ui tool show Matchmaker

> matchmaker #39 to #40

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain C (#40)
with CopZ1_P61924.pdb, chain A (#39), sequence alignment score = 863.4  
RMSD between 141 pruned atom pairs is 0.407 angstroms; (across all 177 pairs:
16.666)  
  

> show #39 models

> hide #40 models

> show #38 models

> show #34 models

> hide #39 models

> hide #38 models

> hide #!25 models

Drag select of 84 residues  

> select up

956 atoms, 971 bonds, 118 residues, 1 model selected  

> select up

9810 atoms, 10032 bonds, 1233 residues, 1 model selected  

> select down

956 atoms, 971 bonds, 118 residues, 1 model selected  
Drag select of 309 residues  

> delete sel

> select clear

[Repeated 2 time(s)]Drag select of 1 pseudobonds  

> delete sel

> select add #34

7345 atoms, 7512 bonds, 2 pseudobonds, 924 residues, 2 models selected  

> select subtract #34

Nothing selected  

> delete sel

> close #34

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopA-F8WHL2.pdb"

CopA-F8WHL2.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit α (F8WHL2) [more
info...]  
  
Chain information for CopA-F8WHL2.pdb #34  
---  
Chain | Description | UniProt  
A | coatomer subunit α | F8WHL2_MOUSE 1-1233  
  
Computing secondary structure  

> show #!25 models

> select add #34

9810 atoms, 10032 bonds, 1233 residues, 1 model selected  

> color sel navy

> ui mousemode right "translate selected models"

> view matrix models #34,1,0,0,139.38,0,1,0,77.792,0,0,1,174.15

> view matrix models #34,1,0,0,143.17,0,1,0,116.78,0,0,1,157.74

> ui mousemode right "rotate selected models"

> view matrix models
> #34,-0.77292,0.46571,-0.43094,110.33,-0.63189,-0.50329,0.58942,111.94,0.057612,0.72788,0.68328,155.75

> view matrix models
> #34,0.095488,0.54565,-0.83256,128.67,-0.72338,-0.53652,-0.43459,118.09,-0.68382,0.64375,0.34348,145.26

> view matrix models
> #34,0.86645,-0.32341,0.38035,140.29,0.26177,0.943,0.20551,120.49,-0.42513,-0.078497,0.90172,151.23

> view matrix models
> #34,-0.13249,-0.98099,-0.14179,130.68,-0.29114,-0.098228,0.95162,112.52,-0.94746,0.16737,-0.27259,148.51

> view matrix models
> #34,-0.191,-0.9337,-0.30287,130.44,-0.10946,-0.28637,0.95185,117.25,-0.97547,0.21495,-0.047502,145.98

> view matrix models
> #34,-0.60871,-0.63739,-0.47244,121.83,0.33431,-0.74608,0.57585,131.6,-0.71952,0.19258,0.66723,145.55

> ui mousemode right "translate selected models"

> view matrix models
> #34,-0.60871,-0.63739,-0.47244,153.15,0.33431,-0.74608,0.57585,151.65,-0.71952,0.19258,0.66723,153.4

> view matrix models
> #34,-0.60871,-0.63739,-0.47244,154.56,0.33431,-0.74608,0.57585,133.83,-0.71952,0.19258,0.66723,140.34

> ui mousemode right "rotate selected models"

> view matrix models
> #34,-0.61566,-0.09401,-0.78238,152.7,0.38273,-0.90356,-0.1926,141.58,-0.68882,-0.41802,0.59227,145.99

> ui mousemode right "translate selected models"

> view matrix models
> #34,-0.61566,-0.09401,-0.78238,154.2,0.38273,-0.90356,-0.1926,117.01,-0.68882,-0.41802,0.59227,135.94

> select up

40776 atoms, 41545 bonds, 5160 residues, 68 models selected  

> select down

9810 atoms, 10032 bonds, 1233 residues, 1 model selected  

> ui mousemode right select

> select clear

> fitmap #34 inMap #25

Fit molecule CopA-F8WHL2.pdb (#34) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 9810 atoms  
average map value = 0.2513, steps = 268  
shifted from previous position = 12.5  
rotated from previous position = 28.3 degrees  
atoms outside contour = 4976, contour level = 0.2532  
  
Position of CopA-F8WHL2.pdb (#34) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.53264139 -0.54606136 -0.64661437 159.40933932  
0.58383331 -0.79018975 0.18638357 127.28571811  
-0.61272491 -0.27823941 0.73969657 133.57411156  
Axis -0.38016417 -0.02772906 0.92450327  
Axis point 83.38396978 99.21518793 0.00000000  
Rotation angle (degrees) 142.33221845  
Shift along axis 59.35847140  
  

> hide #!25 models

Drag select of 204 residues  

> select up

1872 atoms, 1904 bonds, 233 residues, 1 model selected  

> delete sel

Drag select of 67 residues, 2 pseudobonds  
Drag select of 44 residues, 3 pseudobonds  

> select up

515 atoms, 525 bonds, 3 pseudobonds, 65 residues, 2 models selected  

> select up

7938 atoms, 8122 bonds, 3 pseudobonds, 1000 residues, 2 models selected  

> select down

515 atoms, 525 bonds, 3 pseudobonds, 65 residues, 2 models selected  
Drag select of 62 residues, 3 pseudobonds  

> select up

597 atoms, 611 bonds, 3 pseudobonds, 76 residues, 2 models selected  

> delete sel

Drag select of 2 residues  

> select up

645 atoms, 657 bonds, 90 residues, 1 model selected  

> delete sel

> show #!25 models

> fitmap #34 inMap #25

Fit molecule CopA-F8WHL2.pdb (#34) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6696 atoms  
average map value = 0.33, steps = 92  
shifted from previous position = 0.363  
rotated from previous position = 1.55 degrees  
atoms outside contour = 2309, contour level = 0.2532  
  
Position of CopA-F8WHL2.pdb (#34) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.55114104 -0.52745699 -0.64655447 159.68929082  
0.57420657 -0.80195943 0.16476617 126.61771889  
-0.60541752 -0.28044643 0.74486202 133.68887023  
Axis -0.37446301 -0.03459979 0.92659609  
Axis point 83.97786314 98.17305376 0.00000000  
Rotation angle (degrees) 143.52527944  
Shift along axis 59.69690535  
  

> hide #!34 models

> show #35 models

> fitmap #35 inMap #25

Fit molecule CopB_ Q9JIF7.pdb (#35) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 7501 atoms  
average map value = 0.2378, steps = 84  
shifted from previous position = 1.34  
rotated from previous position = 3.2 degrees  
atoms outside contour = 4024, contour level = 0.2532  
  
Position of CopB_ Q9JIF7.pdb (#35) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.32064619 0.78921696 -0.52375815 142.21372577  
0.68088169 -0.57645114 -0.45177892 148.04005904  
-0.65847257 -0.21175615 -0.72220024 154.69062564  
Axis 0.81144623 0.45542974 -0.36624960  
Axis point 0.00000000 24.90601335 113.58992692  
Rotation angle (degrees) 171.49485982  
Shift along axis 126.16525710  
  

> fitmap #35 inMap #25

Fit molecule CopB_ Q9JIF7.pdb (#35) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 7501 atoms  
average map value = 0.2378, steps = 48  
shifted from previous position = 0.00712  
rotated from previous position = 0.00209 degrees  
atoms outside contour = 4022, contour level = 0.2532  
  
Position of CopB_ Q9JIF7.pdb (#35) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.32064133 0.78920396 -0.52378071 142.21243830  
0.68089354 -0.57645720 -0.45175334 148.03333799  
-0.65846269 -0.21178811 -0.72219988 154.68860774  
Axis 0.81144528 0.45542871 -0.36625298  
Axis point 0.00000000 24.90541120 113.58774992  
Rotation angle (degrees) 171.49690419  
Shift along axis 126.16107988  
  

> hide #35 models

> show #36 models

> fitmap #36 inMap #25

Fit molecule CopBprime_O55029.pdb (#36) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 7214 atoms  
average map value = 0.1828, steps = 80  
shifted from previous position = 1.71  
rotated from previous position = 0.68 degrees  
atoms outside contour = 6397, contour level = 0.2532  
  
Position of CopBprime_O55029.pdb (#36) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.50825278 0.05183494 0.85964658 125.87415961  
0.66191789 0.61506689 -0.42843603 193.30517521  
-0.55094811 0.78676926 0.27829898 176.59370632  
Axis 0.62023665 0.71996274 0.31138426  
Axis point 57.84080416 0.00000000 83.07791765  
Rotation angle (degrees) 78.41570987  
Shift along axis 272.23279077  
  

> hide #36 models

> show #36 models

> hide #36 models

> show #37 models

> hide #!25 models

Drag select of 74 residues  

> select up

696 atoms, 711 bonds, 90 residues, 1 model selected  

> delete sel

> select clear

Drag select of 39 residues  

> select up

652 atoms, 661 bonds, 80 residues, 1 model selected  

> delete sel

Drag select of 72 residues, 2 pseudobonds  

> delete sel

> show #!25 models

> select add #25

2 models selected  

> select subtract #25

Nothing selected  

> select add #37

2098 atoms, 2129 bonds, 269 residues, 1 model selected  
Drag select of 25 W20_J4027_005_volume_map_gammazeta_local.mrc , 10 residues  

> select clear

> select add #37

2098 atoms, 2129 bonds, 269 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #37,0.52381,0.45458,-0.7204,159.74,-0.84399,0.16247,-0.51115,164.47,-0.11532,0.87576,0.46877,118.38

> view matrix models
> #37,0.52381,0.45458,-0.7204,159.87,-0.84399,0.16247,-0.51115,160.32,-0.11532,0.87576,0.46877,115.66

> ui mousemode right "rotate selected models"

> view matrix models
> #37,-0.51843,-0.78578,-0.33732,156.47,0.64386,-0.0991,-0.7587,177.15,0.56274,-0.61052,0.55731,131.39

> ui mousemode right "translate selected models"

> view matrix models
> #37,-0.51843,-0.78578,-0.33732,156.82,0.64386,-0.0991,-0.7587,177.21,0.56274,-0.61052,0.55731,131.11

> view matrix models
> #37,-0.51843,-0.78578,-0.33732,169.14,0.64386,-0.0991,-0.7587,188.43,0.56274,-0.61052,0.55731,154.61

> view matrix models
> #37,-0.51843,-0.78578,-0.33732,168.55,0.64386,-0.0991,-0.7587,185.71,0.56274,-0.61052,0.55731,156.17

> fitmap #37 inMap #25

Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 2098 atoms  
average map value = 0.1523, steps = 264  
shifted from previous position = 11.8  
rotated from previous position = 42.5 degrees  
atoms outside contour = 1552, contour level = 0.2532  
  
Position of CopD_full_Q5XJY5.pdb (#37) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.13421510 -0.97879473 -0.15474878 179.22768371  
0.80299796 0.19893091 -0.56180136 174.64912074  
0.58067252 -0.04886073 0.81266971 148.66115690  
Axis 0.25715468 -0.36869186 0.89327363  
Axis point -62.36776041 208.19731599 0.00000000  
Rotation angle (degrees) 85.81897760  
Shift along axis 114.49262034  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #37,0.17652,-0.98345,-0.040823,181.47,0.73295,0.15901,-0.66143,172.16,0.65698,0.086834,0.74889,148.4

> view matrix models
> #37,0.4517,-0.88251,-0.13091,183.25,0.50738,0.3748,-0.77595,166,0.73385,0.28407,0.61707,146.24

> view matrix models
> #37,0.19394,-0.76059,-0.61959,169.31,0.33983,0.64457,-0.68487,164.7,0.92028,-0.077732,0.38347,145.18

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #37,0.13058,-0.95382,-0.27052,176.06,0.41699,0.30039,-0.85784,163.27,0.89948,-0.00078766,0.43696,145.75

> ui mousemode right "translate selected models"

> view matrix models
> #37,0.13058,-0.95382,-0.27052,175.12,0.41699,0.30039,-0.85784,169.65,0.89948,-0.00078766,0.43696,144.2

> view matrix models
> #37,0.13058,-0.95382,-0.27052,176.92,0.41699,0.30039,-0.85784,173.28,0.89948,-0.00078766,0.43696,142.71

> view matrix models
> #37,0.13058,-0.95382,-0.27052,176.07,0.41699,0.30039,-0.85784,171.32,0.89948,-0.00078766,0.43696,141.37

> ui mousemode right "rotate selected models"

> view matrix models
> #37,0.98025,0.13893,0.14075,193.31,0.13603,0.042901,-0.98977,165.4,-0.14355,0.98937,0.023155,115.29

> view matrix models
> #37,-0.70422,-0.31127,-0.63811,154.89,0.39637,-0.91803,0.010376,192.21,-0.58904,-0.24562,0.76987,127.74

> view matrix models
> #37,-0.068744,0.46239,-0.88401,156.66,-0.96301,-0.26218,-0.062249,169.55,-0.26056,0.84703,0.46331,123

> ui mousemode right "translate selected models"

> view matrix models
> #37,-0.068744,0.46239,-0.88401,155.46,-0.96301,-0.26218,-0.062249,163.71,-0.26056,0.84703,0.46331,114.14

> view matrix models
> #37,-0.068744,0.46239,-0.88401,155.61,-0.96301,-0.26218,-0.062249,167.76,-0.26056,0.84703,0.46331,108.27

> view matrix models
> #37,-0.068744,0.46239,-0.88401,151.7,-0.96301,-0.26218,-0.062249,167.34,-0.26056,0.84703,0.46331,109.96

> view matrix models
> #37,-0.068744,0.46239,-0.88401,148.05,-0.96301,-0.26218,-0.062249,168.6,-0.26056,0.84703,0.46331,113.26

> fitmap #37 inMap #25

Fit molecule CopD_full_Q5XJY5.pdb (#37) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 2098 atoms  
average map value = 0.188, steps = 268  
shifted from previous position = 1.8  
rotated from previous position = 31.7 degrees  
atoms outside contour = 1411, contour level = 0.2532  
  
Position of CopD_full_Q5XJY5.pdb (#37) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.10900924 0.75139291 -0.65078850 146.28424526  
-0.97991274 0.02875802 0.19734233 168.20699465  
0.16699701 0.65922808 0.73316460 122.79115227  
Axis 0.23450114 -0.41519279 -0.87899042  
Axis point 141.38224991 -30.78701025 0.00000000  
Rotation angle (degrees) 99.99389905  
Shift along axis -143.46675599  
  

> select subtract #37

Nothing selected  

> hide #!37 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/alphafold 3
> /fold_20240724_copbdg1z1_try2/fold_20240724_copbdg1z1_try2_model_0.cif"

Chain information for fold_20240724_copbdg1z1_try2_model_0.cif #41  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  
Computing secondary structure  

> select add #41

19765 atoms, 20090 bonds, 2515 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #41 to #35

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CopB_ Q9JIF7.pdb, chain A (#35) with
fold_20240724_copbdg1z1_try2_model_0.cif, chain A (#41), sequence alignment
score = 4801.7  
RMSD between 351 pruned atom pairs is 0.825 angstroms; (across all 953 pairs:
12.162)  
  

> fitmap #41 inMap #25

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 19765 atoms  
average map value = 0.1792, steps = 108  
shifted from previous position = 5.04  
rotated from previous position = 8.73 degrees  
atoms outside contour = 12927, contour level = 0.2532  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.76300462 0.02891891 -0.64574581 129.45795402  
0.59375195 -0.42623762 0.68248085 141.01253356  
-0.25550456 -0.90414887 -0.34239193 134.21937577  
Axis -0.91776836 -0.22573072 0.32672141  
Axis point 0.00000000 107.57830339 53.51898785  
Rotation angle (degrees) 120.18624651  
Shift along axis -106.79093220  
  

> hide #!25 models

> view matrix models
> #41,0.75987,0.021282,-0.64972,128.96,0.5945,-0.42707,0.6813,141.3,-0.26298,-0.90397,-0.33717,134.98

> ui mousemode right select

> select clear

> select #37/A

2098 atoms, 2129 bonds, 269 residues, 1 model selected  

> select #41/A

7501 atoms, 7619 bonds, 953 residues, 1 model selected  

> select #41/D

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> delete sel

> select #41/C

6830 atoms, 6947 bonds, 874 residues, 1 model selected  

> delete sel

> fitmap #41 inMap #25

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 11515 atoms  
average map value = 0.1733, steps = 152  
shifted from previous position = 7.6  
rotated from previous position = 10.2 degrees  
atoms outside contour = 7595, contour level = 0.2532  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.72372649 0.02528009 -0.68962373 129.00641102  
0.66961476 -0.26733223 0.69292825 143.29008926  
-0.16684136 -0.96327275 -0.21040333 139.88692109  
Axis -0.89407287 -0.28221546 0.34783348  
Axis point 0.00000000 117.92026971 52.51002968  
Rotation angle (degrees) 112.14825963  
Shift along axis -107.12245762  
  

> show #!25 models

> hide #!25 models

Drag select of 19 residues  

> select up

374 atoms, 380 bonds, 50 residues, 1 model selected  

> select up

4014 atoms, 4083 bonds, 511 residues, 1 model selected  

> select down

374 atoms, 380 bonds, 50 residues, 1 model selected  

> delete sel

Drag select of 24 residues, 2 pseudobonds  

> select up

272 atoms, 278 bonds, 2 pseudobonds, 34 residues, 2 models selected  

> delete sel

Drag select of 46 residues, 2 pseudobonds  

> select up

840 atoms, 846 bonds, 2 pseudobonds, 103 residues, 2 models selected  

> delete sel

Drag select of 81 residues, 2 pseudobonds  
Drag select of 82 residues, 2 pseudobonds  

> select clear

Drag select of 53 residues  

> select up

483 atoms, 487 bonds, 61 residues, 1 model selected  

> select clear

Drag select of 82 residues, 2 pseudobonds  

> select up

844 atoms, 855 bonds, 2 pseudobonds, 108 residues, 2 models selected  

> delete sel

> fitmap #41 inMap #25

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 9185 atoms  
average map value = 0.207, steps = 68  
shifted from previous position = 0.487  
rotated from previous position = 1.21 degrees  
atoms outside contour = 5435, contour level = 0.2532  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.71958143 0.04416992 -0.69300187 128.82756784  
0.67569054 -0.27468426 0.68409856 142.78127561  
-0.16014013 -0.96051943 -0.22750289 139.51471009  
Axis -0.89355970 -0.28951634 0.34312003  
Axis point 0.00000000 115.94606449 53.28137283  
Rotation angle (degrees) 113.03559189  
Shift along axis -108.58234297  
  

> show #!25 models

> hide #!25 models

Drag select of 248 residues  

> select up

2203 atoms, 2233 bonds, 279 residues, 1 model selected  

> delete sel

> fitmap #41 inMap #25

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6982 atoms  
average map value = 0.2082, steps = 260  
shifted from previous position = 7.84  
rotated from previous position = 14 degrees  
atoms outside contour = 4267, contour level = 0.2532  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.60641983 0.19676174 -0.77041535 127.17385378  
0.79490418 -0.12618975 0.59346734 140.58903166  
0.01955314 -0.97229675 -0.23293070 138.75917394  
Axis -0.84500929 -0.42632905 0.32280465  
Axis point 0.00000000 109.24582338 58.49339501  
Rotation angle (degrees) 112.10779478  
Shift along axis -122.60816993  
  

> show #!25 models

> hide #!25 models

Drag select of 85 residues, 1 pseudobonds  

> select up

826 atoms, 836 bonds, 1 pseudobond, 108 residues, 2 models selected  

> delete sel

Drag select of 43 residues  

> select clear

Drag select of 67 residues  

> select up

711 atoms, 719 bonds, 95 residues, 1 model selected  

> delete sel

> fitmap #41 inMap #25

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 5445 atoms  
average map value = 0.1782, steps = 88  
shifted from previous position = 2.03  
rotated from previous position = 3.11 degrees  
atoms outside contour = 3752, contour level = 0.2532  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.60331496 0.23815668 -0.76111264 129.24175666  
0.79728988 -0.15805568 0.58253519 139.72739672  
0.01843647 -0.95827960 -0.28523727 137.10117129  
Axis -0.84890646 -0.42948982 0.30805246  
Axis point 0.00000000 103.56300999 60.01449132  
Rotation angle (degrees) 114.83389261  
Shift along axis -127.49130401  
  

> show #!25 models

> select add #41

5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected  
Drag select of 25 W20_J4027_005_volume_map_gammazeta_local.mrc , 43 residues  

> select clear

> select add #41

5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #41,0.60241,0.22967,-0.76444,137.4,0.7981,-0.15867,0.58126,145.75,0.012205,-0.96025,-0.27888,129.95

> fitmap #41 inMap #25

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#41) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 5445 atoms  
average map value = 0.203, steps = 116  
shifted from previous position = 3.37  
rotated from previous position = 14.2 degrees  
atoms outside contour = 3158, contour level = 0.2532  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#41) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.52191157 0.05705493 -0.85108933 136.78168805  
0.85298460 -0.02899341 0.52113016 146.75941736  
0.00505707 -0.99794996 -0.06379897 132.92819195  
Axis -0.79251134 -0.44665565 0.41524030  
Axis point 0.00000000 120.55875518 58.21435828  
Rotation angle (degrees) 106.58517534  
Shift along axis -118.75481890  
  

> select subtract #41

Nothing selected  

> select add #41

5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected  

> select subtract #41

Nothing selected  

> select add #41

5445 atoms, 5521 bonds, 8 pseudobonds, 687 residues, 2 models selected  

> select subtract #41

Nothing selected  

> show #35 models

> hide #35 models

> ui tool show Matchmaker

> matchmaker #!37 to #41

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_20240724_copbdg1z1_try2_model_0.cif, chain B (#41) with
CopD_full_Q5XJY5.pdb, chain A (#37), sequence alignment score = 2184.5  
RMSD between 114 pruned atom pairs is 0.700 angstroms; (across all 244 pairs:
25.738)  
  

> show #!37 models

> show #35 models

> hide #!41 models

> hide #!25 models

> ui mousemode right rotate

> ui mousemode right select

Drag select of 1 residues  

> select up

184 atoms, 186 bonds, 25 residues, 1 model selected  

> delete sel

> show #!25 models

Drag select of 6 residues  

> select up

483 atoms, 491 bonds, 69 residues, 1 model selected  

> delete sel

> hide #!25 models

> show #!25 models

> show #!34 models

> show #38 models

> show #39 models

> show #36 models

> hide #39 models

> hide #!37 models

> hide #36 models

> hide #35 models

> hide #!34 models

> hide #!25 models

Drag select of 41 residues  

> select up

531 atoms, 541 bonds, 67 residues, 1 model selected  

> delete sel

Drag select of 26 residues, 1 pseudobonds  

> select up

494 atoms, 500 bonds, 1 pseudobond, 64 residues, 2 models selected  

> delete sel

Drag select of 3 residues  

> select up

215 atoms, 218 bonds, 30 residues, 1 model selected  

> delete sel

Drag select of 43 residues, 1 pseudobonds  

> select up

499 atoms, 507 bonds, 1 pseudobond, 62 residues, 2 models selected  

> select clear

Drag select of 23 residues  

> select up

296 atoms, 302 bonds, 36 residues, 1 model selected  
Drag select of 51 residues, 2 pseudobonds  

> select clear

Drag select of 19 residues, 3 pseudobonds  

> select up

167 atoms, 168 bonds, 3 pseudobonds, 20 residues, 2 models selected  

> delete sel

> show #!25 models

> hide #!25 models

Drag select of 33 residues  

> select up

594 atoms, 601 bonds, 75 residues, 1 model selected  

> delete sel

> show #!25 models

> hide #!25 models

Drag select of 65 residues, 3 pseudobonds  

> select up

603 atoms, 610 bonds, 3 pseudobonds, 79 residues, 2 models selected  

> delete sel

> show #!25 models

> fitmap #38 inMap #25

Fit molecule CopG1_ Q9QZE5.pdb (#38) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4226 atoms  
average map value = 0.2729, steps = 96  
shifted from previous position = 0.601  
rotated from previous position = 5.3 degrees  
atoms outside contour = 1993, contour level = 0.2532  
  
Position of CopG1_ Q9QZE5.pdb (#38) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.43244711 0.82798862 0.35696546 106.28810019  
-0.18802207 0.30438532 -0.93380795 122.80007772  
-0.88183740 -0.47093993 0.02404958 119.35137932  
Axis 0.27755203 0.74283001 -0.60923595  
Axis point 83.94095393 0.00000000 76.41437643  
Rotation angle (degrees) 123.50474947  
Shift along axis 48.00691086  
  

> show #39 models

> fitmap #39 inMap #25

Fit molecule CopZ1_P61924.pdb (#39) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms  
average map value = 0.2375, steps = 180  
shifted from previous position = 1.19  
rotated from previous position = 45.5 degrees  
atoms outside contour = 765, contour level = 0.2532  
  
Position of CopZ1_P61924.pdb (#39) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.15949015 0.95372824 0.25488301 116.12737830  
0.29301360 -0.29228658 0.91033598 142.77739950  
0.94271201 -0.07050544 -0.32607217 99.85061617  
Axis -0.71693601 -0.50276157 -0.48294261  
Axis point 0.00000000 31.13613117 -0.38312474  
Rotation angle (degrees) 136.83898997  
Shift along axis -203.26100587  
  

> undo

> show #39 models

> ui tool show Matchmaker

> matchmaker #39 to #40

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain C (#40)
with CopZ1_P61924.pdb, chain A (#39), sequence alignment score = 863.4  
RMSD between 141 pruned atom pairs is 0.407 angstroms; (across all 177 pairs:
16.666)  
  

> select clear

> show #!34 models

> show #35 models

> show #36 models

> show #!37 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

> hide #!25 models

> show #!26 models

> hide #!26 models

> show #!27 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

——— End of log from Tue Jul 1 15:42:09 2025 ———

> view name session-start

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> hide #!27 models

> show #!29 models

> hide #!29 models

> show #!29 models

> volume #29.1 level 0.01218

> volume #29.2 level 0.009354

> volume #29.3 level 0.003817

> volume #29.4 level 0.01012

> hide #!29 models

> show #!29 models

> color #29 silver models

> color #29 darkgrey models

> color #29 #a9a9a9c7 models

> color #29 darkgrey models

> color #29 #929292ff models

> color #29 darkgrey models

> show #!30 models

> volume #30.1 level 0.004859

> hide #!29 models

> color #30 #929292ff models

> volume #30.1 level 0.01271

> volume #30.2 level 0.00973

> volume #30.3 level 0.008159

> volume #30.4 level 0.01229

> hide #!30 models

> show #!31 models

> volume #31.1 level 0.01583

> color #31 #929292ff models

> volume #31.2 level 0.0156

> volume #31.3 level 0.008589

> volume #31.4 level 0.01446

> hide #!31 models

> color #32 #929292ff models

> show #!32 models

> volume #32.1 level 0.01368

> volume #32.3 level 0.01158

> volume #32.4 level 0.01325

> volume #32.2 level 0.01059

> hide #!32 models

> show #!33 models

> volume #33.1 level 0.01263

> color #33 #929292ff models

> volume #33.1 level 0.01481

> volume #33.2 level 0.01481

> volume #33.3 level 0.01517

> volume #33.4 level 0.01344

> hide #!34 models

> hide #35 models

> hide #36 models

> hide #!37 models

> hide #!38 models

> hide #39 models

> show #!41 models

> hide #!41 models

> show #40 models

> hide #40 models

> show #!29 models

> color #29 #8efa00ff models

> color #29 #fffc79ff models

> volume #29.1 level 0.01322

> volume #29.2 level 0.0117

> volume #29.3 level 0.01271

> volume #29.4 level 0.01296

> hide #!29 models

> show #!29 models

> hide #!33 models

> show #!30 models

> hide #!30 models

> show #!31 models

> hide #!31 models

> show #!32 models

> hide #!32 models

> show #!33 models

> show #!32 models

> hide #!32 models

> show #!32 models

> hide #!32 models

> show #!32 models

> hide #!32 models

> show #!32 models

> hide #!33 models

> show #!33 models

> hide #!32 models

> hide #!33 models

> show #!30 models

> hide #!29 models

> volume maximum #30.1 #30.2 #30.3 #30.4

Opened volume maximum as #42, grid size 285,281,252, pixel 1.2, shown at step
1, values float32  

> rename #42 W20_J140_MB

> hide #!42 models

> show #!42 models

> volume maximum #31.1 #31.2 #31.3 #31.4

Opened volume maximum as #43, grid size 248,255,253, pixel 1.2, shown at step
1, values float32  

> rename #43 W20_J145_MB

> hide #!43 models

> show #!43 models

> volume maximum #32.1 #32.2 #32.3 #32.4

Opened volume maximum as #44, grid size 275,269,255, pixel 1.2, shown at step
1, values float32  

> rename #44 W20_J150_MB

> hide #!44 models

> show #!44 models

> volume maximum #33.1 #33.2 #33.3 #33.4

Opened volume maximum as #45, grid size 299,295,317, pixel 1.2, shown at step
1, values float32  

> rename #45 W20_J155_MB

> volume maximum #34.1 #34.2 #34.3 #34.4

[Repeated 3 time(s)]

> close #42

> close #43

> close #44

> close #45

> volume maximum #34.1 #34.2 #34.3 #34.4

> volume maximum #29.1 #29.2 #29.3 #29.4

Opened volume maximum as #42, grid size 281,271,305, pixel 1.2, shown at step
1, values float32  

> volume maximum #30.1 #29.2 #29.3 #29.4

Opened volume maximum as #43, grid size 324,314,331, pixel 1.2, shown at step
1, values float32  

> close #43

> volume maximum #30.1 #30.2 #30.3 #30.4

Opened volume maximum as #43, grid size 285,281,252, pixel 1.2, shown at step
1, values float32  

> volume maximum #31.1 #31.2 #31.3 #31.4

Opened volume maximum as #44, grid size 248,255,253, pixel 1.2, shown at step
1, values float32  

> volume maximum #32.1 #32.2 #32.3 #32.4

Opened volume maximum as #45, grid size 275,269,255, pixel 1.2, shown at step
1, values float32  

> volume maximum #33.1 #33.2 #33.3 #33.4

Opened volume maximum as #46, grid size 299,295,317, pixel 1.2, shown at step
1, values float32  

> rename #42 W20_J140_MB

> rename #42 W20_J140_MB_joined

> rename #43 W20_J145_MB_joined

> rename #44 W20_J150_MB_joined

> rename #45 W20_J155_MB_joined

> rename #46 W20_J160_MB_joined

> fitmap #42 inMap #1

Fit map W20_J140_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 130669 points  
correlation = 0.3924, correlation about mean = 0.006354, overlap = 259.4  
steps = 144, shift = 7.92, angle = 8.21 degrees  
  
Position of W20_J140_MB_joined (#42) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.91620955 0.25591004 -0.30833442 2.94589670  
-0.21484448 0.96327207 0.16108624 14.27677310  
0.33823352 -0.08134481 0.93753993 -22.28584079  
Axis -0.29008545 -0.77366308 -0.56329022  
Axis point 63.49232840 0.00000000 -7.08518329  
Rotation angle (degrees) 24.69964443  
Shift along axis 0.65342200  
  

> fitmap #43 inMap #1

Fit map W20_J145_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 142902 points  
correlation = 0.4199, correlation about mean = 0.04049, overlap = 303  
steps = 164, shift = 1.19, angle = 6.55 degrees  
  
Position of W20_J145_MB_joined (#43) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99583148 0.04008635 0.08193132 -23.34504583  
-0.04315588 0.99841798 0.03604305 -2.05514686  
-0.08035687 -0.03942862 0.99598602 16.93949740  
Axis -0.38234856 0.82217147 -0.42171514  
Axis point 196.57839852 0.00000000 294.50364776  
Rotation angle (degrees) 5.66401964  
Shift along axis 0.09261895  
  

> fitmap #44 inMap #1

Fit map W20_J150_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 100519 points  
correlation = 0.4322, correlation about mean = -0.01831, overlap = 243.2  
steps = 80, shift = 5.66, angle = 2.97 degrees  
  
Position of W20_J150_MB_joined (#44) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99916201 0.02809111 0.02976842 -4.49636094  
-0.03208054 0.98915209 0.14334916 -11.35419842  
-0.02541866 -0.14418402 0.98922437 24.23768179  
Axis -0.96196921 0.18463355 -0.20130992  
Axis point 0.00000000 157.84496089 87.73789734  
Rotation angle (degrees) 8.59507208  
Shift along axis -2.65029098  
  

> fitmap #45 inMap #1

Fit map W20_J155_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 138129 points  
correlation = 0.4135, correlation about mean = 0.03029, overlap = 293.3  
steps = 136, shift = 5.25, angle = 4.6 degrees  
  
Position of W20_J155_MB_joined (#45) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97166385 -0.22776257 -0.06319474 54.87908166  
0.22867640 0.97347338 0.00752908 -17.23256599  
0.05980356 -0.02176688 0.99797281 -6.95123433  
Axis -0.06185438 -0.25969395 0.96370799  
Axis point 107.95346859 225.99227664 0.00000000  
Rotation angle (degrees) 13.69857239  
Shift along axis -5.61827826  
  

> fitmap #46 inMap #1

Fit map W20_J160_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 121938 points  
correlation = 0.4485, correlation about mean = 0.04548, overlap = 303.4  
steps = 176, shift = 10.8, angle = 12.9 degrees  
  
Position of W20_J160_MB_joined (#46) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98515785 -0.09819617 0.14078890 -1.18436719  
0.06853050 0.97700616 0.20189734 -32.23116044  
-0.15737717 -0.18925241 0.96923472 51.60758570  
Axis -0.75318811 0.57414108 0.32104469  
Axis point 0.00000000 244.46953938 184.51242914  
Rotation angle (degrees) 15.05005024  
Shift along axis -1.04484054  
  

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> hide #!42 models

> hide #!43 models

> hide #!44 models

> hide #!45 models

> hide #!46 models

> show #!1 models

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> show #!24 models

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> show #!25 models

> hide #!25 models

> show #!25 models

> color #25 silver models

[Repeated 1 time(s)]

> hide #!25 models

> show #!26 models

> hide #!26 models

> show #!27 models

> hide #!27 models

> show #!28 models

> hide #!28 models

> show #!29 models

> hide #!29 models

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!29 models

> hide #!29 models

> show #!30 models

> hide #!30 models

> show #!30.1 models

> show #!30.2 models

> show #!30.3 models

> show #!30.4 models

> show #!29 models

> hide #!29 models

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!29.1 models

> show #!29.2 models

> show #!29.3 models

> show #!29.4 models

> hide #!29 models

> show #!31 models

> show #!31.1 models

> show #!31.2 models

> show #!31.3 models

> show #!31.4 models

> hide #!31 models

> show #!31 models

> hide #!31 models

> show #!31 models

> hide #!31 models

> show #!32 models

> show #!32.1 models

> show #!32.2 models

> show #!32.3 models

> show #!32.4 models

> hide #!32 models

> select add #32

9 models selected  

> select subtract #32

Nothing selected  

> show #!32 models

> hide #!32 models

> show #!33 models

> show #!33.1 models

> show #!33.2 models

> show #!33.3 models

> show #!33.4 models

> hide #!33 models

> show #!32 models

> hide #!32 models

> show #!33 models

> hide #!33 models

> show #!42 models

> hide #!42 models

> show #!42 models

> show #!43 models

> hide #!43 models

> select add #42

2 models selected  

> view matrix models
> #42,0.91621,0.25591,-0.30833,6.5795,-0.21484,0.96327,0.16109,11.618,0.33823,-0.081345,0.93754,-14.738

> ui mousemode right "rotate selected models"

> view matrix models
> #42,-0.20075,-0.93591,0.28944,250.09,-0.75521,0.33604,0.5628,121.07,-0.62399,-0.10561,-0.77426,360.31

> ui mousemode right "translate selected models"

> view matrix models
> #42,-0.20075,-0.93591,0.28944,258.45,-0.75521,0.33604,0.5628,111.09,-0.62399,-0.10561,-0.77426,373.71

> ui mousemode right "rotate selected models"

> view matrix models
> #42,-0.33018,-0.9414,-0.068949,327.26,-0.81305,0.24654,0.52742,137.15,-0.47951,0.2302,-0.8468,314.67

> fitmap #42 inMap #1

Fit map W20_J140_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 130669 points  
correlation = 0.8803, correlation about mean = 0.3684, overlap = 1189  
steps = 172, shift = 19.9, angle = 7.77 degrees  
  
Position of W20_J140_MB_joined (#42) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.35155267 -0.92578085 -0.13907028 347.82271473  
-0.76197836 0.19666262 0.61701928 136.35497869  
-0.54387471 0.32288331 -0.77456224 286.91060622  
Axis -0.55865111 0.76884323 0.31110933  
Axis point 248.45663259 0.00000000 85.56946066  
Rotation angle (degrees) 164.73667959  
Shift along axis -0.21537821  
  

> select subtract #42

Nothing selected  

> hide #!42 models

> show #!43 models

> select add #43

2 models selected  

> view matrix models
> #43,-0.71667,-0.59905,-0.3571,362.32,-0.66464,0.43155,0.60993,81.644,-0.21127,0.67446,-0.70744,174.56

> view matrix models
> #43,-0.22267,-0.96408,0.14484,277.38,-0.843,0.26503,0.46809,150.16,-0.48966,-0.017866,-0.87173,336.37

> ui mousemode right "translate selected models"

> view matrix models
> #43,-0.22267,-0.96408,0.14484,278.5,-0.843,0.26503,0.46809,152.18,-0.48966,-0.017866,-0.87173,341.6

> fitmap #43 inMap #1

Fit map W20_J145_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 142902 points  
correlation = 0.8839, correlation about mean = 0.3912, overlap = 1241  
steps = 176, shift = 16.1, angle = 20.5 degrees  
  
Position of W20_J145_MB_joined (#43) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33273365 -0.93244330 -0.14084678 345.90650730  
-0.76625576 0.18027360 0.61672809 139.19380919  
-0.54967302 0.31313085 -0.77447314 289.28503932  
Axis -0.56677541 0.76322385 0.31024988  
Axis point 250.48919740 0.00000000 85.44391549  
Rotation angle (degrees) 164.46490776  
Shift along axis -0.06461673  
  

> select subtract #43

Nothing selected  

> hide #!43 models

> show #!44 models

> select add #44

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #44,-0.64334,-0.25066,-0.72339,371.34,-0.44115,0.89362,0.082686,67.718,0.62571,0.37232,-0.68547,101.18

> view matrix models
> #44,-0.33974,-0.91968,0.1969,294.7,-0.6214,0.37665,0.68702,81.003,-0.706,0.11106,-0.69945,324.73

> view matrix models
> #44,-0.34685,-0.93744,0.029929,322.46,-0.77694,0.30504,0.55074,132.64,-0.52542,0.16777,-0.83414,311.06

> ui mousemode right "translate selected models"

> view matrix models
> #44,-0.34685,-0.93744,0.029929,328.6,-0.77694,0.30504,0.55074,126.41,-0.52542,0.16777,-0.83414,322.03

> fitmap #44 inMap #1

Fit map W20_J150_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 100519 points  
correlation = 0.8806, correlation about mean = 0.2563, overlap = 1060  
steps = 104, shift = 9.91, angle = 11.1 degrees  
  
Position of W20_J150_MB_joined (#44) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34988200 -0.92650940 -0.13843016 347.22501351  
-0.75857847 0.19350448 0.62218544 135.60290867  
-0.54967381 0.32270162 -0.77053382 287.77852170  
Axis -0.55901416 0.76762419 0.31345858  
Axis point 248.55561653 0.00000000 85.33747140  
Rotation angle (degrees) 164.46257054  
Shift along axis 0.19501983  
  

> select subtract #44

Nothing selected  

> hide #!44 models

> show #!45 models

> ui mousemode right "rotate selected models"

> select add #45

2 models selected  

> view matrix models
> #45,-0.93945,-0.28966,-0.18313,341.27,-0.33735,0.87568,0.34552,26.538,0.060286,0.38637,-0.92037,203.81

> view matrix models
> #45,-0.39594,-0.91199,0.10724,318.12,-0.72625,0.38247,0.57121,120.46,-0.56195,0.14828,-0.81377,308.66

> fitmap #45 inMap #1

Fit map W20_J155_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 138129 points  
correlation = 0.8776, correlation about mean = 0.3767, overlap = 1250  
steps = 140, shift = 15.4, angle = 15.9 degrees  
  
Position of W20_J155_MB_joined (#45) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.35675611 -0.91947462 -0.16520144 351.40689174  
-0.78155048 0.19688467 0.59195886 143.25471986  
-0.51176551 0.34029820 -0.78885563 282.02499467  
Axis -0.55929726 0.77021311 0.30652624  
Axis point 248.57307844 0.00000000 86.50174383  
Rotation angle (degrees) 166.99833687  
Shift along axis 0.24381166  
  

> select subtract #45

Nothing selected  

> hide #!45 models

> show #!46 models

> select add #46

2 models selected  

> view matrix models
> #46,-0.25068,-0.94965,-0.18794,340.4,-0.93649,0.1887,0.29561,209.1,-0.24527,0.25011,-0.93664,265.98

> view matrix models
> #46,-0.071284,-0.98257,0.17165,270.25,-0.5959,0.17996,0.78264,95.4,-0.79989,-0.046498,-0.59834,338.43

> ui mousemode right "translate selected models"

> view matrix models
> #46,-0.071284,-0.98257,0.17165,275.5,-0.5959,0.17996,0.78264,90.643,-0.79989,-0.046498,-0.59834,355.66

> view matrix models
> #46,-0.071284,-0.98257,0.17165,285.03,-0.5959,0.17996,0.78264,91.932,-0.79989,-0.046498,-0.59834,362.22

> fitmap #46 inMap #1

Fit map W20_J160_MB_joined in map W20_J3623_consensus_structure_sharp.mrc
using 121938 points  
correlation = 0.8667, correlation about mean = 0.3087, overlap = 1157  
steps = 208, shift = 18.2, angle = 31.4 degrees  
  
Position of W20_J160_MB_joined (#46) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.39178850 -0.90130925 -0.18477932 357.17449457  
-0.76159854 0.20502417 0.61476235 135.64467847  
-0.51620677 0.38158448 -0.76676193 274.65181077  
Axis -0.54399036 0.77320089 0.32593693  
Axis point 245.55803639 0.00000000 83.69005707  
Rotation angle (degrees) 167.62426420  
Shift along axis 0.10027404  
  

> select subtract #46

Nothing selected  

> hide #!46 models

> show #!46 models

> hide #!46 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

——— End of log from Wed Jul 2 15:03:33 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!1 models

> show #!46 models

> show #!45 models

> show #!25 models

> color #25 #ff2600ff models

> color #46 #ff9300ff models

> color #45 #fffb00ff models

> show #!9 models

> color #9 #8efa00ff models

> show #!27 models

> color #27 #00fdffff models

> show #!23 models

> color #23 #0433ffff models

> hide #!27 models

> show #!27 models

> hide #!27 models

> hide #!25 models

> hide #!23 models

> hide #!9 models

> hide #!45 models

> hide #!46 models

> show #!46 models

> show #!23 models

> hide #!46 models

> hide #!23 models

> show #!46 models

> hide #!1 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"

——— End of log from Wed Jul 2 17:43:06 2025 ———

opened ChimeraX session  

> color list

28 custom colors: alphav1

, alphav2

, alphav3

, arf1v1

, arf1v2

, arf1v3

, betapv1

, betapv2

, betapv3

, betav1

, betav2

, betav3

, deltav1

, deltav2

, deltav3

, epsilonv1

, epsilonv3

, gammav1

, gammav2

, gammav3

, label_purple

, label_purple_v3

, label_red

, label_red_v3

, lable_purple_v4

, zetav1

, zetav2

, and zetav3

.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color name gamma_1 #5EAF5A

Color 'gamma_1' is opaque: rgb(36.9%, 68.6%, 35.3%) hex: #5eaf5a

  

> color name gamma_2 #83CA6B

Color 'gamma_2' is opaque: rgb(51.4%, 79.2%, 42%) hex: #83ca6b

  

> color name gamma_3 #ADE57C

Color 'gamma_3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c

  

> color name gamma_4 #C9EA8C

Color 'gamma_4' is opaque: rgb(78.8%, 91.8%, 54.9%) hex: #c9ea8c

  

> color name gamma_5 #E1EF9C

Color 'gamma_5' is opaque: rgb(88.2%, 93.7%, 61.2%) hex: #e1ef9c

  

> color name gamma_6 #F3FIAD

Missing or invalid "color" argument: expected hexadecimal digits after #  

> color name gamma_6 #F3F1AD

Color 'gamma_6' is opaque: rgb(95.3%, 94.5%, 67.8%) hex: #f3f1ad

  

> show #!45 models

> hide #!45 models

> hide #!46 models

> show #!46 models

> show #!45 models

> show #!25 models

> hide #!46 models

> hide #!45 models

> show #!38 models

> show #35 models

> color #25 silver models

> color #25 #c0c0c074 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/W20_C1_initial_model_v3.pdb"

Chain information for W20_C1_initial_model_v3.pdb #47  
---  
Chain | Description  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> select add #47

28705 atoms, 29239 bonds, 3 pseudobonds, 3615 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> hide #!38 models

> hide #35 models

> view matrix models #47,1,0,0,-79.232,0,1,0,36.623,0,0,1,9.1376

> view matrix models #47,1,0,0,-13.804,0,1,0,-20.445,0,0,1,10.191

> view matrix models #47,1,0,0,0.72332,0,1,0,-4.6589,0,0,1,-2.6371

> fitmap #47 inMap #1

Fit molecule W20_C1_initial_model_v3.pdb (#47) to map
W20_J3623_consensus_structure_sharp.mrc (#1) using 28705 atoms  
average map value = 0.301, steps = 80  
shifted from previous position = 5.02  
rotated from previous position = 0.504 degrees  
atoms outside contour = 16132, contour level = 0.26383  
  
Position of W20_C1_initial_model_v3.pdb (#47) relative to
W20_J3623_consensus_structure_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99996809 -0.00526689 0.00600723 0.01730039  
0.00528904 0.99997925 -0.00367710 -0.57665128  
-0.00598774 0.00370875 0.99997520 0.14412341  
Axis 0.41958417 0.68142506 0.59967410  
Axis point 54.13790036 0.00000000 -23.49447330  
Rotation angle (degrees) 0.50428904  
Shift along axis -0.29925859  
  

> select subtract #47

Nothing selected  

> hide #!47 models

> show #!47 models

> split #47 chains

Split W20_C1_initial_model_v3.pdb (#47) into 9 models  
Chain information for W20_C1_initial_model_v3.pdb D #47.1  
---  
Chain | Description  
D | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb E #47.2  
---  
Chain | Description  
E | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb F #47.3  
---  
Chain | Description  
F | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb G #47.4  
---  
Chain | Description  
G | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb H #47.5  
---  
Chain | Description  
H | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb I #47.6  
---  
Chain | Description  
I | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb J #47.7  
---  
Chain | Description  
J | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb K #47.8  
---  
Chain | Description  
K | No description available  
  
Chain information for W20_C1_initial_model_v3.pdb L #47.9  
---  
Chain | Description  
L | No description available  
  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250703_W20_COPI_cyto_alignments.cxs"

——— End of log from Thu Jul 3 17:41:19 2025 ———

opened ChimeraX session  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/FlexFit_W20_C1_initial_model_v3/W20_C1_initial_model_v3_no_wat_lig.pdb"

Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb #48  
---  
Chain | Description  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #47.1-5,9#!48#!47.6-8 atoms

> show #47.1-5,9#!48#!47.6-8 cartoons

> hide #!47 models

> hide #!48 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/RIBFIND_W20_C1_initial_model_v3/W20_C1_initial_model_v3_no_wat_lig.pdb"

Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb #49  
---  
Chain | Description  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!49 atoms

> show #!49 cartoons

> show #!48 models

> hide #!48 models

> show #!47 models

> hide #!47 models

> hide #!49 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/Icknield_workshop_files/W20_models/FlexFit_W20_C1_initial_model_TEMPyReff_flexfit/W20_C1_initial_model_no_wat_lig.pdb"

Chain information for W20_C1_initial_model_no_wat_lig.pdb #50  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
BA | No description available  
  

> hide #!50 atoms

> show #!50 cartoons

> select add #50

25890 atoms, 26364 bonds, 22 pseudobonds, 3243 residues, 2 models selected  

> select subtract #50

Nothing selected  

> ui tool show Matchmaker

> matchmaker #!50 to #34

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CopA-F8WHL2.pdb, chain A (#34) with
W20_C1_initial_model_no_wat_lig.pdb, chain A2 (#50), sequence alignment score
= 2196.3  
RMSD between 303 pruned atom pairs is 0.597 angstroms; (across all 445 pairs:
4.918)  
  

> hide #!25 models

> show #!7 models

> hide #!7 models

> show #!25 models

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> show #!7 models

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> hide #!7 models

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/A_fixed_model_2_A.pdb

Summary of feedback from opening
/Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/A_fixed_model_2_A.pdb  
---  
warning | Ignored bad PDB record found on line 9748  
  
Chain information for A_fixed_model_2_A.pdb #51  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/B_fixed_model_2_B.pdb

Summary of feedback from opening
/Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/B_fixed_model_2_B.pdb  
---  
warning | Ignored bad PDB record found on line 7507  
  
Chain information for B_fixed_model_2_B.pdb #52  
---  
Chain | Description  
B | No description available  
  
Computing secondary structure  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/C1_fixed_model_2_C1.pdb

Summary of feedback from opening
/Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/C1_fixed_model_2_C1.pdb  
---  
warning | Ignored bad PDB record found on line 3967  
  
Chain information for C1_fixed_model_2_C1.pdb #53  
---  
Chain | Description  
C1 | No description available  
  
Computing secondary structure  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/D1_fixed_model_2_D1.pdb

Summary of feedback from opening
/Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/D1_fixed_model_2_D1.pdb  
---  
warning | Ignored bad PDB record found on line 3307  
  
Chain information for D1_fixed_model_2_D1.pdb #54  
---  
Chain | Description  
D1 | No description available  
  
Computing secondary structure  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/E2_full_shifted_sm_1.pdb

Summary of feedback from opening
/Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/E2_full_shifted_sm_1.pdb  
---  
warning | Ignored bad PDB record found on line 4486  
  
Chain information for E2_full_shifted_sm_1.pdb #55  
---  
Chain | Description  
E2 | No description available  
  
Computing secondary structure  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/F_fixed_model_2_F.pdb

Summary of feedback from opening
/Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1/local_dock_and_rebuild_6_1/run_mr/F_fixed_model_2_F.pdb  
---  
warning | Ignored bad PDB record found on line 1426  
  
Chain information for F_fixed_model_2_F.pdb #56  
---  
Chain | Description  
F | No description available  
  
Computing secondary structure  

> hide #!25 models

> show #!1 models

> hide #56 models

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> hide #51 models

> hide #!1 models

> show #!2 models

> color #2 darkgrey models

> color #2 #a9a9a980 models

> hide #!50 models

> show #!47 models

> fitmap #47 inMap #2

Fit molecules W20_C1_initial_model_v3.pdb D (#47.1),
W20_C1_initial_model_v3.pdb E (#47.2), W20_C1_initial_model_v3.pdb F (#47.3),
W20_C1_initial_model_v3.pdb G (#47.4), W20_C1_initial_model_v3.pdb H (#47.5),
W20_C1_initial_model_v3.pdb I (#47.6), W20_C1_initial_model_v3.pdb J (#47.7),
W20_C1_initial_model_v3.pdb K (#47.8), W20_C1_initial_model_v3.pdb L (#47.9)
to map W20_J3623_consensus_structure.mrc (#2) using 28705 atoms  
average map value = 0.26, steps = 44  
shifted from previous position = 0.0505  
rotated from previous position = 0.167 degrees  
atoms outside contour = 16402, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb D (#47.1) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb E (#47.2) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb F (#47.3) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb G (#47.4) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb H (#47.5) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb I (#47.6) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb J (#47.7) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb K (#47.8) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  
Position of W20_C1_initial_model_v3.pdb L (#47.9) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995987 -0.00698720 0.00560699 0.30640707  
0.00699483 0.99997464 -0.00134153 -1.12673692  
-0.00559747 0.00138070 0.99998338 0.47678248  
Axis 0.15020785 0.61824110 0.77150214  
Axis point 136.27032262 49.14800743 0.00000000  
Rotation angle (degrees) 0.51919628  
Shift along axis -0.28273161  
  

> fitmap #47.1 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb D (#47.1) to map
W20_J3623_consensus_structure.mrc (#2) using 4763 atoms  
average map value = 0.3391, steps = 60  
shifted from previous position = 0.277  
rotated from previous position = 0.317 degrees  
atoms outside contour = 1269, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb D (#47.1) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99993645 -0.00554192 0.00981798 -0.36993206  
0.00552327 0.99998289 0.00192574 -1.44337504  
-0.00982849 -0.00187139 0.99994995 1.45151156  
Axis -0.16606190 0.85921136 0.48392075  
Axis point 170.89777041 0.00000000 46.84174593  
Rotation angle (degrees) 0.65506824  
Shift along axis -0.47631604  
  

> fitmap #47.2 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb E (#47.2) to map
W20_J3623_consensus_structure.mrc (#2) using 1856 atoms  
average map value = 0.298, steps = 52  
shifted from previous position = 0.74  
rotated from previous position = 0.516 degrees  
atoms outside contour = 807, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb E (#47.2) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99985158 -0.01068491 0.01351472 -0.71801951  
0.01073315 0.99993626 -0.00350238 -1.71551668  
-0.01347643 0.00364691 0.99990254 2.22722625  
Axis 0.20315994 0.76700206 0.60863280  
Axis point 169.67451772 0.00000000 53.39691400  
Rotation angle (degrees) 1.00818411  
Shift along axis -0.10611466  
  

> fitmap #47.3 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb F (#47.3) to map
W20_J3623_consensus_structure.mrc (#2) using 7214 atoms  
average map value = 0.1919, steps = 56  
shifted from previous position = 0.863  
rotated from previous position = 1.3 degrees  
atoms outside contour = 5840, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb F (#47.3) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99983282 -0.01767194 -0.00469422 4.64975550  
0.01774465 0.99971568 0.01592750 -6.16380107  
0.00441141 -0.01600813 0.99986213 2.74940793  
Axis -0.65778440 -0.18755047 0.72948236  
Axis point 350.49529384 263.63816940 0.00000000  
Rotation angle (degrees) 1.39100037  
Shift along axis 0.10313173  
  

> fitmap #47.4 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb G (#47.4) to map
W20_J3623_consensus_structure.mrc (#2) using 1872 atoms  
average map value = 0.2684, steps = 48  
shifted from previous position = 0.694  
rotated from previous position = 1.52 degrees  
atoms outside contour = 902, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb G (#47.4) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999905 0.00004391 -0.00137935 0.08316312  
-0.00001180 0.99972908 0.02327568 -3.69665287  
0.00138000 -0.02327564 0.99972813 3.29847865  
Axis -0.99824711 -0.05917154 -0.00119461  
Axis point 0.00000000 139.85035535 160.11317726  
Rotation angle (degrees) 1.33605990  
Shift along axis 0.13177890  
  

> fitmap #47.5 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb H (#47.5) to map
W20_J3623_consensus_structure.mrc (#2) using 4752 atoms  
average map value = 0.2052, steps = 56  
shifted from previous position = 0.558  
rotated from previous position = 2.67 degrees  
atoms outside contour = 3635, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb H (#47.5) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99873328 -0.02416117 0.04413700 -1.58450683  
0.02335616 0.99955296 0.01866451 -4.67495439  
-0.04456822 -0.01760999 0.99885112 6.98195313  
Axis -0.33911247 0.82926157 0.44421615  
Axis point 157.93980007 0.00000000 42.26069084  
Rotation angle (degrees) 3.06589704  
Shift along axis -0.23793767  
  

> fitmap #47.6 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb I (#47.6) to map
W20_J3623_consensus_structure.mrc (#2) using 2488 atoms  
average map value = 0.3942, steps = 48  
shifted from previous position = 0.0985  
rotated from previous position = 0.351 degrees  
atoms outside contour = 688, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb I (#47.6) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99997623 -0.00687548 -0.00051167 1.19535071  
0.00687477 0.99997543 -0.00137176 -1.17275950  
0.00052109 0.00136821 0.99999893 -0.25085656  
Axis 0.19489694 -0.07346086 0.97806886  
Axis point 170.41255683 171.17704205 0.00000000  
Rotation angle (degrees) 0.40275148  
Shift along axis 0.07376713  
  

> fitmap #47.7 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb J (#47.7) to map
W20_J3623_consensus_structure.mrc (#2) using 2879 atoms  
average map value = 0.2974, steps = 40  
shifted from previous position = 0.0947  
rotated from previous position = 0.56 degrees  
atoms outside contour = 1205, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb J (#47.7) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99998391 0.00266199 0.00500985 -1.32620675  
-0.00264770 0.99999241 -0.00285677 0.77420871  
-0.00501741 0.00284346 0.99998337 0.17173811  
Axis 0.44891807 0.78969202 -0.41816155  
Axis point 28.71795251 0.00000000 259.81340923  
Rotation angle (degrees) 0.36376436  
Shift along axis -0.05578601  
  

> fitmap #47.8 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb K (#47.8) to map
W20_J3623_consensus_structure.mrc (#2) using 1681 atoms  
average map value = 0.2582, steps = 2000  
shifted from previous position = 3.05  
rotated from previous position = 19.1 degrees  
atoms outside contour = 877, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb K (#47.8) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.94200137 -0.31946272 0.10284450 49.35608426  
0.31956519 0.94743045 0.01592570 -41.58693728  
-0.10252568 0.01786349 0.99456995 13.43084868  
Axis 0.00288696 0.30596518 0.95203833  
Axis point 151.23068995 127.03929522 0.00000000  
Rotation angle (degrees) 19.60965973  
Shift along axis 0.20501701  
  

> fitmap #47.9 inMap #2

Fit molecule W20_C1_initial_model_v3.pdb L (#47.9) to map
W20_J3623_consensus_structure.mrc (#2) using 1200 atoms  
average map value = 0.225, steps = 104  
shifted from previous position = 7.72  
rotated from previous position = 16.8 degrees  
atoms outside contour = 923, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3.pdb L (#47.9) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95622273 0.06913903 0.28435522 -32.79890580  
-0.07184973 0.99741506 -0.00090016 15.80706570  
-0.28368241 -0.01957009 0.95871857 38.27014130  
Axis -0.03188330 0.97005801 -0.24077150  
Axis point 121.59404774 0.00000000 133.26118376  
Rotation angle (degrees) 17.02478724  
Shift along axis 7.16514893  
  

> hide #!47 models

> show #!48 models

> split #48 chains

Split W20_C1_initial_model_v3_no_wat_lig.pdb (#48) into 9 models  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb D #48.1  
---  
Chain | Description  
D | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb E #48.2  
---  
Chain | Description  
E | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb F #48.3  
---  
Chain | Description  
F | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb G #48.4  
---  
Chain | Description  
G | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb H #48.5  
---  
Chain | Description  
H | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb I #48.6  
---  
Chain | Description  
I | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb J #48.7  
---  
Chain | Description  
J | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb K #48.8  
---  
Chain | Description  
K | No description available  
  
Chain information for W20_C1_initial_model_v3_no_wat_lig.pdb L #48.9  
---  
Chain | Description  
L | No description available  
  

> fitmap #48.9 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb L (#48.9) to map
W20_J3623_consensus_structure.mrc (#2) using 1200 atoms  
average map value = 0.225, steps = 104  
shifted from previous position = 7.35  
rotated from previous position = 17 degrees  
atoms outside contour = 923, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb L (#48.9) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95618362 0.06935484 0.28443415 -32.83561380  
-0.07187151 0.99741263 -0.00159273 15.88500353  
-0.28380868 -0.01891977 0.95869426 38.21611444  
Axis -0.02957914 0.97005222 -0.24108871  
Axis point 121.32947981 0.00000000 133.38706461  
Rotation angle (degrees) 17.03122986  
Shift along axis 7.16705836  
  

> fitmap #48.8 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb K (#48.8) to map
W20_J3623_consensus_structure.mrc (#2) using 1681 atoms  
average map value = 0.2582, steps = 2000  
shifted from previous position = 3  
rotated from previous position = 19.6 degrees  
atoms outside contour = 877, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb K (#48.8) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.94200226 -0.31945879 0.10284856 49.35474105  
0.31956109 0.94743180 0.01592780 -41.58682474  
-0.10253028 0.01786237 0.99456949 13.43178853  
Axis 0.00288219 0.30598035 0.95203347  
Axis point 151.23135956 127.03695546 0.00000000  
Rotation angle (degrees) 19.60950766  
Shift along axis 0.20501096  
  

> fitmap #48.7 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb J (#48.7) to map
W20_J3623_consensus_structure.mrc (#2) using 2879 atoms  
average map value = 0.2974, steps = 60  
shifted from previous position = 0.232  
rotated from previous position = 0.38 degrees  
atoms outside contour = 1205, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb J (#48.7) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99998287 0.00312090 0.00495157 -1.40345048  
-0.00310539 0.99999025 -0.00313821 0.88665991  
-0.00496131 0.00312278 0.99998282 0.10130440  
Axis 0.47162964 0.74671971 -0.46901508  
Axis point 14.97777640 0.00000000 278.97871593  
Rotation angle (degrees) 0.38031035  
Shift along axis -0.04733570  
  

> fitmap #48.6 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb I (#48.6) to map
W20_J3623_consensus_structure.mrc (#2) using 2488 atoms  
average map value = 0.3942, steps = 68  
shifted from previous position = 0.638  
rotated from previous position = 0.407 degrees  
atoms outside contour = 688, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb I (#48.6) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99997568 -0.00695350 -0.00053467 1.20906358  
0.00695275 0.99997488 -0.00137680 -1.17749870  
0.00054423 0.00137305 0.99999891 -0.25259458  
Axis 0.19342635 -0.07589115 0.97817523  
Axis point 169.14439112 171.16881708 0.00000000  
Rotation angle (degrees) 0.40727684  
Shift along axis 0.07614472  
  

> fitmap #48.5 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb H (#48.5) to map
W20_J3623_consensus_structure.mrc (#2) using 4752 atoms  
average map value = 0.2052, steps = 56  
shifted from previous position = 0.398  
rotated from previous position = 3.04 degrees  
atoms outside contour = 3633, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb H (#48.5) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99875256 -0.02376142 0.04391712 -1.59501966  
0.02297566 0.99956832 0.01831081 -4.59906082  
-0.04433325 -0.01727895 0.99886736 6.92788561  
Axis -0.33570594 0.83243532 0.44085481  
Axis point 157.55390321 0.00000000 42.61926354  
Rotation angle (degrees) 3.03852113  
Shift along axis -0.23877143  
  

> fitmap #48.4 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb G (#48.4) to map
W20_J3623_consensus_structure.mrc (#2) using 1872 atoms  
average map value = 0.2684, steps = 52  
shifted from previous position = 0.66  
rotated from previous position = 1.34 degrees  
atoms outside contour = 904, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb G (#48.4) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999668 -0.00055774 -0.00251381 0.32378285  
0.00061619 0.99972807 0.02331118 -3.79263384  
0.00250012 -0.02331266 0.99972510 3.13991886  
Axis -0.99395584 -0.10688996 0.02502646  
Axis point 0.00000000 132.58526090 163.49903175  
Rotation angle (degrees) 1.34391993  
Shift along axis 0.16214970  
  

> fitmap #48.3 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb F (#48.3) to map
W20_J3623_consensus_structure.mrc (#2) using 7214 atoms  
average map value = 0.1919, steps = 52  
shifted from previous position = 1.21  
rotated from previous position = 1.38 degrees  
atoms outside contour = 5841, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb F (#48.3) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99983183 -0.01777810 -0.00449952 4.61473624  
0.01784647 0.99971839 0.01564141 -6.12537351  
0.00422018 -0.01571908 0.99986754 2.73144245  
Axis -0.64988004 -0.18069744 0.73824411  
Axis point 346.08368056 260.84380532 -0.00000000  
Rotation angle (degrees) 1.38256144  
Shift along axis 0.12428563  
  

> fitmap #48.2 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb E (#48.2) to map
W20_J3623_consensus_structure.mrc (#2) using 1856 atoms  
average map value = 0.298, steps = 48  
shifted from previous position = 0.513  
rotated from previous position = 0.756 degrees  
atoms outside contour = 811, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb E (#48.2) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99991922 -0.00558717 0.01141652 -1.06360279  
0.00562764 0.99997799 -0.00351551 -0.81089288  
-0.01139663 0.00357947 0.99992865 1.85466537  
Axis 0.26882817 0.86438839 0.42492838  
Axis point 169.58714833 0.00000000 89.68331202  
Rotation angle (degrees) 0.75610423  
Shift along axis -0.19875283  
  

> fitmap #48.1 inMap #2

Fit molecule W20_C1_initial_model_v3_no_wat_lig.pdb D (#48.1) to map
W20_J3623_consensus_structure.mrc (#2) using 4763 atoms  
average map value = 0.3391, steps = 52  
shifted from previous position = 0.556  
rotated from previous position = 0.656 degrees  
atoms outside contour = 1271, contour level = 0.25746  
  
Position of W20_C1_initial_model_v3_no_wat_lig.pdb D (#48.1) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99993657 -0.00557361 0.00978726 -0.36204539  
0.00555366 0.99998245 0.00206434 -1.46156620  
-0.00979859 -0.00200985 0.99994997 1.46464333  
Axis -0.17797856 0.85559501 0.48608724  
Axis point 172.75674812 0.00000000 46.73299778  
Rotation angle (degrees) 0.65580741  
Shift along axis -0.47412801  
  

> hide #!48 models

> show #!49 models

> hide #!49 models

> show #!50 models

> fitmap #50 inMap #2

Fit molecule W20_C1_initial_model_no_wat_lig.pdb (#50) to map
W20_J3623_consensus_structure.mrc (#2) using 25890 atoms  
average map value = 0.2892, steps = 92  
shifted from previous position = 6.37  
rotated from previous position = 6 degrees  
atoms outside contour = 13101, contour level = 0.25746  
  
Position of W20_C1_initial_model_no_wat_lig.pdb (#50) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.92962183 0.23756050 -0.28172373 363.07149255  
-0.02176229 -0.79853926 -0.60154921 515.96615164  
-0.36787180 -0.55308232 0.74750939 166.87632524  
Axis 0.17464117 0.31041809 -0.93442018  
Axis point 215.59521690 272.59770300 0.00000000  
Rotation angle (degrees) 172.02382323  
Shift along axis 67.63985482  
  

> show #51 models

> hide #51 models

> hide #!50 models

> show #!50 models

> split #50 chains

Split W20_C1_initial_model_no_wat_lig.pdb (#50) into 11 models  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A0 #50.1  
---  
Chain | Description  
A0 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A1 #50.2  
---  
Chain | Description  
A1 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A2 #50.3  
---  
Chain | Description  
A2 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A3 #50.4  
---  
Chain | Description  
A3 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A4 #50.5  
---  
Chain | Description  
A4 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A5 #50.6  
---  
Chain | Description  
A5 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A6 #50.7  
---  
Chain | Description  
A6 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A7 #50.8  
---  
Chain | Description  
A7 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A8 #50.9  
---  
Chain | Description  
A8 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb A9 #50.10  
---  
Chain | Description  
A9 | No description available  
  
Chain information for W20_C1_initial_model_no_wat_lig.pdb BA #50.11  
---  
Chain | Description  
BA | No description available  
  

> hide #50.1 models

> show #50.1 models

> hide #50.1 models

> show #50.1 models

> hide #!50.2 models

> show #!50.2 models

> hide #!50.2 models

> show #!50.2 models

> hide #!50.3 models

> show #!50.3 models

> hide #!50.4 models

> show #!50.4 models

> hide #!50.3 models

> show #!50.3 models

> ui tool show Matchmaker

> matchmaker #51 to #50.3

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A2, chain A2 (#50.3) with
A_fixed_model_2_A.pdb, chain A (#51), sequence alignment score = 2192.7  
RMSD between 285 pruned atom pairs is 0.343 angstroms; (across all 445 pairs:
7.570)  
  

> show #51 models

> hide #!50.7 models

> show #!50.7 models

> ui tool show Matchmaker

> show #52 models

> hide #52 models

> show #!53 models

> matchmaker #!53 to #50.7

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A6, chain A6 (#50.7) with
C1_fixed_model_2_C1.pdb, chain C1 (#53), sequence alignment score = 1136.3  
RMSD between 188 pruned atom pairs is 0.567 angstroms; (across all 446 pairs:
42.070)  
  

> hide #!53 models

> show #!54 models

> hide #!50.8 models

> show #!50.8 models

> hide #!50.8 models

> show #!50.8 models

> ui tool show Matchmaker

> hide #50.6 models

> show #50.6 models

> hide #!50.4 models

> show #!50.4 models

> matchmaker #52 to #50.4

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A3, chain A3 (#50.4) with
B_fixed_model_2_B.pdb, chain B (#52), sequence alignment score = 2854.3  
RMSD between 172 pruned atom pairs is 0.254 angstroms; (across all 567 pairs:
4.295)  
  

> show #52 models

> hide #52 models

> ui tool show Matchmaker

> matchmaker #!54 to #50.8

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A7, chain A7 (#50.8) with
D1_fixed_model_2_D1.pdb, chain D1 (#54), sequence alignment score = 660  
RMSD between 129 pruned atom pairs is 0.312 angstroms; (across all 131 pairs:
0.453)  
  

> hide #!54 models

> show #!55 models

> hide #!55 models

> show #!55 models

> hide #!50.10 models

> show #!50.10 models

> hide #!50.10 models

> show #!50.10 models

> ui tool show Matchmaker

> matchmaker #!55 to #50.10

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A9, chain A9 (#50.10) with
E2_full_shifted_sm_1.pdb, chain E2 (#55), sequence alignment score = 1394.2  
RMSD between 277 pruned atom pairs is 0.670 angstroms; (across all 277 pairs:
0.670)  
  

> hide #!55 models

> show #!55 models

> hide #!55 models

> show #!55 models

> hide #!50.10 models

> show #!50.10 models

> hide #!55 models

> show #56 models

> hide #50.11 models

> show #50.11 models

> ui tool show Matchmaker

> matchmaker #56 to #50.11

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb BA, chain BA (#50.11) with
F_fixed_model_2_F.pdb, chain F (#56), sequence alignment score = 725  
RMSD between 144 pruned atom pairs is 0.244 angstroms; (across all 144 pairs:
0.244)  
  

> hide #56 models

> hide #51 models

> show #36 models

> hide #36 models

> show #36 models

> hide #36 models

> show #36 models

> hide #36 models

> show #35 models

> hide #35 models

> show #52 models

> fitmap #52 inMap #2

Fit molecule B_fixed_model_2_B.pdb (#52) to map
W20_J3623_consensus_structure.mrc (#2) using 7500 atoms  
average map value = 0.316, steps = 88  
shifted from previous position = 2.73  
rotated from previous position = 5.83 degrees  
atoms outside contour = 2940, contour level = 0.25746  
  
Position of B_fixed_model_2_B.pdb (#52) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.33624269 -0.92088355 -0.19726715 276.34525406  
-0.77887628 0.15416253 0.60793557 158.89643495  
-0.52942667 0.35806060 -0.76909038 243.62727331  
Axis -0.56887772 0.75621078 0.32330079  
Axis point 214.85544208 0.00000000 65.79075689  
Rotation angle (degrees) 167.31322736  
Shift along axis 41.71742887  
  

> fitmap #50.112

Missing required "in_map" argument  

> fitmap #50.11 inMap #2

Fit molecule W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) to map
W20_J3623_consensus_structure.mrc (#2) using 1158 atoms  
average map value = 0.2425, steps = 216  
shifted from previous position = 24  
rotated from previous position = 39.5 degrees  
atoms outside contour = 674, contour level = 0.25746  
  
Position of W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.96490741 -0.23836579 -0.11016098 456.74587096  
0.21274833 -0.46373391 -0.86005174 403.93698444  
0.15392153 -0.85330687 0.49817221 176.52114975  
Axis 0.01290218 -0.50515953 0.86292954  
Axis point 197.70794601 288.88132577 0.00000000  
Rotation angle (degrees) 164.84772556  
Shift along axis -45.83428628  
  

> show #56 models

> hide #56 models

> show #56 models

> hide #56 models

> ui tool show Matchmaker

> matchmaker #50.11 to #56

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker F_fixed_model_2_F.pdb, chain F (#56) with
W20_C1_initial_model_no_wat_lig.pdb BA, chain BA (#50.11), sequence alignment
score = 725  
RMSD between 144 pruned atom pairs is 0.244 angstroms; (across all 144 pairs:
0.244)  
  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

> hide #!2 models

> hide #!50 models

> show #!50 models

> hide #52 models

> show #!53 models

> hide #!53 models

> show #!54 models

> hide #!54 models

> show #!54 models

> hide #!54 models

> show #!55 models

> hide #!55 models

> show #52 models

> show #!33 models

> color #33 #b2b2b290 models

> color #33 #b2b2b28f models

> hide #52 models

> show #52 models

> hide #!50.8 models

> show #!50.8 models

> hide #50.6 models

> show #50.6 models

> hide #!50.4 models

> hide #!50.8 models

> show #!50.8 models

> fitmap #50.8 inMap #2

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) to map
W20_J3623_consensus_structure.mrc (#2) using 1057 atoms  
average map value = 0.2692, steps = 56  
shifted from previous position = 0.944  
rotated from previous position = 4.88 degrees  
atoms outside contour = 542, contour level = 0.25746  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.93105828 0.16643564 -0.32469934 390.48149308  
0.06181231 -0.80509185 -0.58992064 497.62568127  
-0.35959661 -0.56932091 0.73929966 170.58533102  
Axis 0.18360289 0.31103515 -0.93249510  
Axis point 219.20897097 271.57117220 0.00000000  
Rotation angle (degrees) 176.78409911  
Shift along axis 67.40262593  
  
Must specify one map, got 4  

> hide #!50.8 models

> show #!50.8 models

> hide #!33 models

> show #!46 models

> show #!33 models

> hide #!46 models

> hide #!33.4 models

> show #!33.4 models

> hide #!33.3 models

> show #!33.3 models

> hide #!33.2 models

> show #!33.2 models

> hide #!33.1 models

> show #!33.1 models

> fitmap #50.8 inMap #33.1

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 1057 atoms  
average map value = 0.01137, steps = 52  
shifted from previous position = 0.606  
rotated from previous position = 3.76 degrees  
atoms outside contour = 692, contour level = 0.014811  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.93056714 0.15394973 -0.33218109 390.44774590  
0.14816644 -0.67132819 -0.72619912 477.44064772  
-0.33480069 -0.72499513 0.60190577 233.60614941  
Axis 0.18631674 0.40538097 -0.89495941  
Axis point 219.95045580 291.28468198 0.00000000  
Rotation angle (degrees) 179.81487490  
Shift along axis 57.22428050  
  

> hide #!50.8 models

> show #!50.8 models

> hide #50.9 models

> show #50.9 models

> hide #!50.8 models

> show #!50.8 models

> select add #50.8

1057 atoms, 1072 bonds, 1 pseudobond, 131 residues, 2 models selected  

> view matrix models
> #50.8,-0.90846,0.21715,-0.35712,384.12,0.037606,-0.80851,-0.58728,501.46,-0.41627,-0.54695,0.72634,175.24

> ui mousemode right "rotate selected models"

> view matrix models
> #50.8,-0.98593,-0.16588,0.020652,396.52,0.059686,-0.46474,-0.88344,489.6,0.15614,-0.86977,0.4681,195.56

> fitmap #50.8 inMap #33.1

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 1057 atoms  
average map value = 0.01486, steps = 88  
shifted from previous position = 2.12  
rotated from previous position = 17.4 degrees  
atoms outside contour = 497, contour level = 0.014811  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A7 (#50.8) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.98685430 0.03145837 0.15852120 311.01536433  
-0.16062302 -0.29929277 -0.94054457 509.24173521  
0.01785625 -0.95364260 0.30041129 284.21437212  
Axis -0.05493227 0.58993953 -0.80557668  
Axis point 163.53469015 347.02960176 0.00000000  
Rotation angle (degrees) 173.15292285  
Shift along axis 54.38058021  
  

> select subtract #50.8

Nothing selected  

> fitmap #50.7 inMap #33.1

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 4264 atoms  
average map value = 0.005768, steps = 160  
shifted from previous position = 2.43  
rotated from previous position = 3.77 degrees  
atoms outside contour = 3553, contour level = 0.014811  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.95014016 0.15038437 -0.27316336 382.66549579  
0.08966442 -0.70725915 -0.70124517 487.55197868  
-0.29865360 -0.69077423 0.65851119 202.15694868  
Axis 0.15703122 0.38227356 -0.91060865  
Axis point 213.00898151 282.79480162 0.00000000  
Rotation angle (degrees) 178.08938676  
Shift along axis 62.38279471  
  

> hide #50.11 models

> show #50.11 models

> fitmap #50.11inMap #33.3

Missing or invalid "atomsOrMap" argument: only initial part "#50.11" of atom
specifier valid  

> fitmap #50.11 inMap #33.3

Fit molecule W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 1158 atoms  
average map value = 0.0132, steps = 104  
shifted from previous position = 5.13  
rotated from previous position = 28.7 degrees  
atoms outside contour = 711, contour level = 0.015167  
  
Position of W20_C1_initial_model_no_wat_lig.pdb BA (#50.11) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
-0.92321344 -0.13158780 -0.36105621 489.23124927  
0.28319718 -0.86806041 -0.40776278 396.62096334  
-0.25976200 -0.47870218 0.83867033 84.55689237  
Axis -0.16389770 -0.23402916 0.95831513  
Axis point 230.41567989 235.72565549 0.00000000  
Rotation angle (degrees) 167.50152307  
Shift along axis -91.97259645  
  

> hide #50.11 models

> show #39 models

> fitmap #39 inMap #33.3

Fit molecule CopZ1_P61924.pdb (#39) to map W20_J160_run_ct6_body003.mrc
(#33.3) using 1420 atoms  
average map value = 0.01141, steps = 92  
shifted from previous position = 7.91  
rotated from previous position = 10.3 degrees  
atoms outside contour = 963, contour level = 0.015167  
  
Position of CopZ1_P61924.pdb (#39) relative to W20_J160_run_ct6_body003.mrc
(#33.3) coordinates:  
Matrix rotation and translation  
-0.50106153 0.84740615 0.17561366 128.97282199  
-0.08865073 -0.25211715 0.96362752 130.68154277  
0.86085911 0.46726840 0.20144938 92.25448210  
Axis -0.39337422 -0.54307030 -0.74184323  
Axis point 46.59255051 18.60088904 0.00000000  
Rotation angle (degrees) 140.88349075  
Shift along axis -190.14221075  
  

> select add #39

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> view matrix models
> #39,-0.038392,0.25438,0.96634,124.66,0.50314,-0.8306,0.23864,135.53,0.86335,0.49537,-0.096103,99.479

> fitmap #39 inMap #33.3

Fit molecule CopZ1_P61924.pdb (#39) to map W20_J160_run_ct6_body003.mrc
(#33.3) using 1420 atoms  
average map value = 0.0138, steps = 140  
shifted from previous position = 3.19  
rotated from previous position = 29.8 degrees  
atoms outside contour = 768, contour level = 0.015167  
  
Position of CopZ1_P61924.pdb (#39) relative to W20_J160_run_ct6_body003.mrc
(#33.3) coordinates:  
Matrix rotation and translation  
-0.59910220 0.35688559 0.71673513 128.54412804  
0.33901457 -0.69789676 0.63087974 127.78779026  
0.72535901 0.62094508 0.29712207 93.14122293  
Axis -0.44768773 -0.38862007 -0.80532611  
Axis point 38.57930905 41.25889004 0.00000000  
Rotation angle (degrees) 179.36426033  
Shift along axis -182.21758707  
  

> select subtract #39

Nothing selected  

> show #!34 models

> hide #!34 models

> show #!34 models

> hide #!34 models

> hide #39 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> hide #50.1 models

> show #!50 models

> hide #!50 models

> hide #52 models

> show #!34 models

> fitmap #33 inMap #33.3

Multiple maps for #33  

> fitmap #34 inMap #33.2

Fit molecule CopA-F8WHL2.pdb (#34) to map W20_J160_run_ct6_body002.mrc (#33.2)
using 6696 atoms  
average map value = 0.01229, steps = 144  
shifted from previous position = 0.768  
rotated from previous position = 0.619 degrees  
atoms outside contour = 4035, contour level = 0.014809  
  
Position of CopA-F8WHL2.pdb (#34) relative to W20_J160_run_ct6_body002.mrc
(#33.2) coordinates:  
Matrix rotation and translation  
-0.57247775 -0.57456895 -0.58492714 151.44699314  
0.70447239 -0.70969024 0.00764404 125.42515832  
-0.41950911 -0.40768897 0.81104982 121.20707602  
Axis -0.30653667 -0.12208683 0.94399686  
Axis point 68.14146734 105.20078411 -0.00000000  
Rotation angle (degrees) 137.35447863  
Shift along axis 52.68228363  
  

> show #50.1 models

> hide #50.1 models

> show #50.1 models

> hide #!50 models

> hide #50.1 models

> show #!50 models

> show #50.1 models

> hide #!50.3 models

> show #!50.3 models

> hide #!50.5 models

> hide #!50.2 models

> hide #!50.3 models

> hide #50.6 models

> hide #!50.8 models

> hide #50.9 models

> hide #!50.7 models

> hide #!50.10 models

> hide #50.1 models

> show #!50.2 models

> show #!50.3 models

> fitmap #50.2 inMap #33.2

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A1 (#50.2) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 2510 atoms  
average map value = 0.01804, steps = 44  
shifted from previous position = 0.476  
rotated from previous position = 0.223 degrees  
atoms outside contour = 1048, contour level = 0.014809  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A1 (#50.2) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.95004228 0.18207545 -0.25351172 368.13646707  
0.07472194 -0.65592625 -0.75111742 494.19899480  
-0.30304504 -0.73253620 0.60955264 227.59862474  
Axis 0.15525602 0.41387719 -0.89699567  
Axis point 211.61727753 293.61074195 0.00000000  
Rotation angle (degrees) 176.56933670  
Shift along axis 57.53811301  
  

> fitmap #50.3 inMap #33.2

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 3559 atoms  
average map value = 0.01022, steps = 184  
shifted from previous position = 2.7  
rotated from previous position = 7.42 degrees  
atoms outside contour = 2357, contour level = 0.014809  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.93274721 0.18386833 -0.31012106 379.03416947  
0.07603460 -0.74050966 -0.66773063 496.69481023  
-0.35242216 -0.64640381 0.67672796 193.41619316  
Axis 0.18107201 0.35915085 -0.91554552  
Axis point 216.23338293 280.38752423 0.00000000  
Rotation angle (degrees) 176.62387365  
Shift along axis 69.93951212  
  

> hide #!33 models

> hide #!34 models

> show #!34 models

> hide #!50.2 models

> show #!50.2 models

> hide #!50.2 models

> ui mousemode right select

Drag select of 223 residues  

> select up

2109 atoms, 2166 bonds, 262 residues, 1 model selected  

> select up

6696 atoms, 6852 bonds, 834 residues, 1 model selected  

> select down

2109 atoms, 2166 bonds, 262 residues, 1 model selected  

> select #34/A:127

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 1 residues  

> select up

6696 atoms, 6852 bonds, 834 residues, 1 model selected  

> select down

8 atoms, 1 residue, 1 model selected  
Drag select of 190 residues  

> select up

1664 atoms, 1710 bonds, 206 residues, 1 model selected  

> select up

6696 atoms, 6852 bonds, 834 residues, 1 model selected  

> select down

1664 atoms, 1710 bonds, 206 residues, 1 model selected  

> delete sel

Drag select of 63 residues, 2 pseudobonds  

> select up

788 atoms, 803 bonds, 2 pseudobonds, 96 residues, 2 models selected  

> delete sel

Drag select of 19 residues, 2 pseudobonds  

> delete sel

Drag select of 4 residues  

> delete sel

> show #!50.2 models

> show #!33 models

> fitmap #34 inMap #33.2

Fit molecule CopA-F8WHL2.pdb (#34) to map W20_J160_run_ct6_body002.mrc (#33.2)
using 4046 atoms  
average map value = 0.009675, steps = 164  
shifted from previous position = 0.697  
rotated from previous position = 2.08 degrees  
atoms outside contour = 2782, contour level = 0.014809  
  
Position of CopA-F8WHL2.pdb (#34) relative to W20_J160_run_ct6_body002.mrc
(#33.2) coordinates:  
Matrix rotation and translation  
-0.58668811 -0.55339986 -0.59122387 151.25489618  
0.67908972 -0.73393831 0.01310416 124.24263215  
-0.44117369 -0.39380599 0.80640103 120.81607944  
Axis -0.31143421 -0.11484294 0.94330262  
Axis point 69.89652487 102.51139715 0.00000000  
Rotation angle (degrees) 139.21031634  
Shift along axis 52.59178621  
  

> fitmap #50.3 inMap #33.2

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 3559 atoms  
average map value = 0.01022, steps = 160  
shifted from previous position = 0.0132  
rotated from previous position = 0.015 degrees  
atoms outside contour = 2353, contour level = 0.014809  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A2 (#50.3) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.93280742 0.18368258 -0.31005003 379.08438259  
0.07605879 -0.74062741 -0.66759726 496.69733667  
-0.35225754 -0.64632171 0.67689207 193.32199255  
Axis 0.18099805 0.35907301 -0.91559067  
Axis point 216.22488098 280.37147530 0.00000000  
Rotation angle (degrees) 176.63062081  
Shift along axis 69.96032790  
  

> combine #34

> combine #50.3

> hide #!50.3 models

> hide #!34 models

> hide #!33.4 models

> show #!33.4 models

> hide #!33 models

> hide #!58 models

> select clear

> hide #!50.2 models

Drag select of 243 residues  

> select up

2056 atoms, 2095 bonds, 259 residues, 1 model selected  

> select up

4046 atoms, 4125 bonds, 509 residues, 1 model selected  

> select up

101979 atoms, 103831 bonds, 12855 residues, 91 models selected  

> select clear

Drag select of 274 residues  

> select up

2192 atoms, 2235 bonds, 276 residues, 1 model selected  

> delete sel

Drag select of 2 residues, 1 pseudobonds  

> delete sel

> show #!33 models

> fitmap #57 inMap #33.1

Fit molecule copy of CopA-F8WHL2.pdb (#57) to map W20_J160_run_ct6_body001.mrc
(#33.1) using 1842 atoms  
average map value = 0.01399, steps = 76  
shifted from previous position = 7.58  
rotated from previous position = 11.9 degrees  
atoms outside contour = 1005, contour level = 0.014811  
  
Position of copy of CopA-F8WHL2.pdb (#57) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.66070189 -0.61639558 -0.42840344 148.88789464  
0.70166098 -0.70992235 -0.06068050 124.32932168  
-0.26672999 -0.34068570 0.90154776 127.22528478  
Axis -0.20632088 -0.11912853 0.97120548  
Axis point 61.04505270 103.19655495 0.00000000  
Rotation angle (degrees) 137.26821223  
Shift along axis 78.03204323  
  

> hide #!57 models

> hide #!33.4 models

> show #!33.4 models

> hide #!33 models

> show #!58 models

Drag select of 104 residues, 1 pseudobonds  

> select clear

Drag select of 282 residues, 6 pseudobonds  

> delete sel

> fitmap #87 inMap #33.1

No atoms or maps for #87  

> fitmap #58 inMap #33.1

Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A2 (#58) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 1297 atoms  
average map value = 0.01501, steps = 108  
shifted from previous position = 10.8  
rotated from previous position = 12.4 degrees  
atoms outside contour = 664, contour level = 0.014811  
  
Position of copy of W20_C1_initial_model_no_wat_lig.pdb A2 (#58) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.95774575 0.09731996 -0.27065088 396.29244001  
0.15737130 -0.61033953 -0.77635039 474.71597461  
-0.24074332 -0.78613897 0.56923472 242.75449330  
Axis -0.14438058 -0.44113353 0.88575135  
Axis point 213.60576536 301.52927607 0.00000000  
Rotation angle (degrees) 178.05738481  
Shift along axis -51.60994703  
  

> show #!33 models

> show #!57 models

> hide #!58 models

> show #!58 models

> hide #!57 models

> show #!57 models

> hide #!33 models

> show #!34 models

> hide #!57 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!58 models

Drag select of 144 residues  

> select clear

[Repeated 1 time(s)]

> combine #34

> hide #!34 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!58 models

Drag select of 161 residues  

> select up

1359 atoms, 1382 bonds, 172 residues, 1 model selected  

> show #!58 models

> hide #!58 models

> delete sel

Drag select of 9 residues  

> delete sel

> fitmap #59 inMap #33.1

Fit molecule copy of CopA-F8WHL2.pdb (#59) to map W20_J160_run_ct6_body001.mrc
(#33.1) using 2618 atoms  
average map value = 0.00517, steps = 108  
shifted from previous position = 1.61  
rotated from previous position = 4.74 degrees  
atoms outside contour = 2287, contour level = 0.014811  
  
Position of copy of CopA-F8WHL2.pdb (#59) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.61097397 -0.53341027 -0.58496522 151.41100776  
0.68780030 -0.72352924 -0.05861913 123.94831007  
-0.39197139 -0.43815401 0.80893726 122.28836749  
Axis -0.29346029 -0.14922482 0.94425262  
Axis point 69.10859861 104.04335802 0.00000000  
Rotation angle (degrees) 139.71015631  
Shift along axis 52.54182884  
  

> fitmap #59 inMap #33.2

Fit molecule copy of CopA-F8WHL2.pdb (#59) to map W20_J160_run_ct6_body002.mrc
(#33.2) using 2618 atoms  
average map value = 0.0148, steps = 72  
shifted from previous position = 1.57  
rotated from previous position = 4.66 degrees  
atoms outside contour = 1354, contour level = 0.014809  
  
Position of copy of CopA-F8WHL2.pdb (#59) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.58463217 -0.55176650 -0.59477640 151.19300478  
0.68006639 -0.73305905 0.01158206 124.19731133  
-0.44239681 -0.39771619 0.80380775 120.82904766  
Axis -0.31316702 -0.11659043 0.94251424  
Axis point 69.96688260 102.62111999 0.00000000  
Rotation angle (degrees) 139.19532441  
Shift along axis 52.05421740  
  

> show #!33 models

> show #!58 models

> show #!50.2 models

> hide #!33 models

> show #!34 models

> hide #!34 models

> show #!34 models

> hide #!34 models

> show #!34 models

> hide #!34 models

> show #!34 models

> hide #!50.2 models

> show #!50.2 models

> hide #!34 models

> show #!34 models

> hide #!34 models

> show #!34 models

> hide #!34 models

> hide #!59 models

> show #!59 models

> show #!57 models

> hide #!57 models

> show #!57 models

> hide #!57 models

> hide #!59 models

> show #!57 models

> hide #!58 models

> hide #!57 models

> show #!33 models

> show #!57 models

> show #!58 models

> hide #!58 models

> show #!59 models

> hide #!59 models

> show #!59 models

> hide #!57 models

> show #!58 models

> hide #!33 models

> show #51 models

> combine #51

> hide #51 models

> hide #!59 models

> hide #!58 models

> hide #!50.2 models

Drag select of 667 residues  

> select up

6183 atoms, 6300 bonds, 784 residues, 1 model selected  

> delete sel

Drag select of 87 residues, 10 pseudobonds  

> select clear

Drag select of 61 residues, 5 pseudobonds  

> select up

758 atoms, 752 bonds, 5 pseudobonds, 95 residues, 2 models selected  

> delete sel

Drag select of 27 residues, 3 pseudobonds  

> select up

2800 atoms, 2874 bonds, 3 pseudobonds, 345 residues, 2 models selected  

> select down

210 atoms, 3 pseudobonds, 27 residues, 2 models selected  

> delete sel

> fitmap #60 inMap #33.2

Fit molecule copy of A_fixed_model_2_A.pdb (#60) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 2590 atoms  
average map value = 0.01604, steps = 212  
shifted from previous position = 8.36  
rotated from previous position = 37.7 degrees  
atoms outside contour = 1297, contour level = 0.014809  
  
Position of copy of A_fixed_model_2_A.pdb (#60) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.12666898 -0.97960527 -0.15597590 240.27472629  
0.03811656 -0.16193319 0.98606530 35.82542257  
-0.99121244 0.11895862 0.05785109 200.76320490  
Axis -0.55003121 0.52981504 0.64557082  
Axis point 195.41347917 29.75172699 0.00000000  
Rotation angle (degrees) 127.97921254  
Shift along axis 16.42911600  
  

> show #!33 models

> show #50.1 models

> hide #50.1 models

> show #!50.2 models

> select add #60

2590 atoms, 2665 bonds, 318 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #60,-0.3575,-0.93077,-0.076565,262.87,-0.90319,0.36543,-0.22518,271.82,0.23757,-0.011349,-0.9713,201.17

> ui tool show Matchmaker

> matchmaker #!60 to #50.2

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A1, chain A1 (#50.2) with copy
of A_fixed_model_2_A.pdb, chain A (#60), sequence alignment score = 1588.3  
RMSD between 296 pruned atom pairs is 0.254 angstroms; (across all 296 pairs:
0.254)  
  

> hide #!50.2 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> select subtract #60

Nothing selected  

> show #!50.2 models

> show #51 models

> hide #51 models

> show #51 models

> hide #51 models

> combine #51

> hide #!33 models

> hide #!50.2 models

> hide #!60 models

> ui mousemode right select

Drag select of 103 residues  

> select up

1168 atoms, 1193 bonds, 145 residues, 1 model selected  

> delete sel

> hide #!61 models

> show #!60 models

> hide #!60 models

> show #!61 models

> select #61/A:318

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 47 bonds, 6 residues, 1 model selected  

> select up

7736 atoms, 7896 bonds, 978 residues, 1 model selected  

> select down

47 atoms, 47 bonds, 6 residues, 1 model selected  

> delete sel

Drag select of 100 residues, 3 pseudobonds  

> select up

1091 atoms, 1121 bonds, 3 pseudobonds, 134 residues, 2 models selected  

> select down

793 atoms, 3 pseudobonds, 100 residues, 2 models selected  

> select clear

> select #61/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

533 atoms, 549 bonds, 64 residues, 1 model selected  

> delete sel

Drag select of 9 residues, 1 pseudobonds  

> delete sel

Drag select of 26 residues, 1 pseudobonds  

> select up

258 atoms, 264 bonds, 1 pseudobond, 33 residues, 2 models selected  

> delete sel

Drag select of 7 residues  

> select clear

[Repeated 1 time(s)]Drag select of 13 residues  
Drag select of 48 residues  

> select up

507 atoms, 517 bonds, 62 residues, 1 model selected  

> select down

384 atoms, 48 residues, 1 model selected  

> select clear

Drag select of 50 residues  

> select up

507 atoms, 517 bonds, 62 residues, 1 model selected  

> select clear

Drag select of 1 residues  

> select up

42 atoms, 42 bonds, 6 residues, 1 model selected  

> delete sel

> select #61/A:263

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

44 atoms, 43 bonds, 6 residues, 1 model selected  

> delete sel

> select clear

> select #61/A:258

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 4 residues  

> select clear

Drag select of 4 residues  

> select clear

Drag select of 5 residues  

> select up

121 atoms, 122 bonds, 14 residues, 1 model selected  

> delete sel

> select clear

> select #61/A:273

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

54 atoms, 55 bonds, 6 residues, 1 model selected  

> delete sel

> select #61/A:278

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 1 residues  
Drag select of 6 residues  

> select up

90 atoms, 90 bonds, 11 residues, 1 model selected  

> fitmap #60 inMap #33.2

Fit molecule copy of A_fixed_model_2_A.pdb (#60) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 2590 atoms  
average map value = 0.01743, steps = 48  
shifted from previous position = 0.0339  
rotated from previous position = 0.278 degrees  
atoms outside contour = 1142, contour level = 0.014809  
  
Position of copy of A_fixed_model_2_A.pdb (#60) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.44176945 -0.87418787 -0.20158210 278.02704219  
-0.65633376 0.16174616 0.73692889 133.70992844  
-0.61160916 0.45785781 -0.64521352 224.98469771  
Axis -0.51515506 0.75689501 0.40215074  
Axis point 203.25110647 0.00000000 49.34812669  
Rotation angle (degrees) 164.28447736  
Shift along axis 48.45510328  
  

> delete sel

Drag select of 16 residues, 1 pseudobonds  

> select up

205 atoms, 209 bonds, 1 pseudobond, 25 residues, 2 models selected  

> select down

126 atoms, 1 pseudobond, 16 residues, 2 models selected  

> delete sel

Drag select of 2 residues  

> delete sel

> show #!60 models

> show #!33 models

> fitmap #61 inMap #33.1

Fit molecule copy of A_fixed_model_2_A.pdb (#61) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 7151 atoms  
average map value = 0.004441, steps = 228  
shifted from previous position = 5.35  
rotated from previous position = 8.58 degrees  
atoms outside contour = 6297, contour level = 0.014811  
  
Position of copy of A_fixed_model_2_A.pdb (#61) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.45222649 -0.82892764 -0.32919625 288.15586650  
-0.57376739 -0.01220253 0.81892739 121.44819917  
-0.68284858 0.55922273 -0.47009335 215.98047971  
Axis -0.51166679 0.69676128 0.50271344  
Axis point 206.53531672 0.00000000 35.33484489  
Rotation angle (degrees) 165.29851626  
Shift along axis 45.75690645  
  

> fitmap #61 inMap #33.2

Fit molecule copy of A_fixed_model_2_A.pdb (#61) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 7151 atoms  
average map value = 0.005548, steps = 2000  
shifted from previous position = 4.46  
rotated from previous position = 9.55 degrees  
atoms outside contour = 5855, contour level = 0.014809  
  
Position of copy of A_fixed_model_2_A.pdb (#61) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.32348189 -0.90777241 -0.26703693 271.47554220  
-0.61054188 -0.01536719 0.79183487 128.17226278  
-0.72290946 0.41918147 -0.54926207 231.58959567  
Axis -0.56499205 0.69116330 0.45064096  
Axis point 214.35725794 0.00000000 37.95145878  
Rotation angle (degrees) 160.74418801  
Shift along axis 39.57019701  
  

> combine #61

> hide #!61 models

> hide #!60 models

> hide #!50 models

> show #!50 models

> hide #!33 models

Drag select of 1 residues  

> select up

7151 atoms, 7294 bonds, 906 residues, 1 model selected  

> select clear

Drag select of 169 residues  

> select up

1541 atoms, 1568 bonds, 193 residues, 1 model selected  

> delete sel

Drag select of 51 residues, 1 pseudobonds  

> select up

646 atoms, 657 bonds, 1 pseudobond, 82 residues, 2 models selected  

> delete sel

Drag select of 4 residues  

> select clear

Drag select of 3 residues  

> select clear

[Repeated 2 time(s)]Drag select of 20 residues, 2 pseudobonds  

> select up

796 atoms, 812 bonds, 2 pseudobonds, 108 residues, 2 models selected  

> delete sel

Drag select of 8 residues, 1 pseudobonds  

> select clear

Drag select of 15 residues  

> delete sel

> select clear

> delete sel

> select clear

> delete sel

> close #62

> combine #61

Drag select of 269 residues  

> select up

2282 atoms, 2326 bonds, 286 residues, 1 model selected  

> delete sel

Drag select of 37 residues, 2 pseudobonds  

> select up

738 atoms, 753 bonds, 2 pseudobonds, 101 residues, 2 models selected  

> delete sel

Drag select of 10 residues  

> delete sel

> close #62

> combine #61

> select clear

[Repeated 1 time(s)]

> select #62/A:873

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 1 residues  

> select up

645 atoms, 657 bonds, 90 residues, 1 model selected  

> delete sel

Drag select of 309 residues  

> delete sel

> fitmap #62 inMap #33.1

Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 4038 atoms  
average map value = 0.007876, steps = 128  
shifted from previous position = 3.44  
rotated from previous position = 10.8 degrees  
atoms outside contour = 3167, contour level = 0.014811  
  
Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.49233635 -0.83165726 -0.25680949 286.92215484  
-0.53267730 0.05454857 0.84455867 111.52201588  
-0.68837476 0.55260352 -0.46986119 217.04968179  
Axis -0.48600137 0.71840251 0.49769518  
Axis point 201.81367843 0.00000000 36.66306761  
Rotation angle (degrees) 162.52050103  
Shift along axis 48.69771641  
  

> show #!33 models

> hide #!62 models

> show #!62 models

> hide #!62 models

> show #!60 models

> show #!61 models

> hide #!61 models

> show #!61 models

> show #!62 models

> hide #!62 models

> show #!62 models

> hide #!62 models

> close #61

> show #!62 models

> combine #62

> hide #!62 models

> hide #!60 models

> fitmap #61 inMap #33.2

Fit molecule copy of copy of copy of A_fixed_model_2_A.pdb (#61) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 4038 atoms  
average map value = 0.009974, steps = 196  
shifted from previous position = 3.26  
rotated from previous position = 10.9 degrees  
atoms outside contour = 2744, contour level = 0.014809  
  
Position of copy of copy of copy of A_fixed_model_2_A.pdb (#61) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.32106500 -0.91005872 -0.26212669 270.65425094  
-0.60680985 -0.01482211 0.79470882 127.10234227  
-0.72711696 0.41421424 -0.54747373 232.51552841  
Axis -0.56535652 0.69090415 0.45058125  
Axis point 214.25644692 0.00000000 38.06080511  
Rotation angle (degrees) 160.33570313  
Shift along axis 39.56652768  
  

> hide #!33 models

> show #!33 models

> hide #!33 models

Drag select of 10 residues  

> select up

388 atoms, 400 bonds, 50 residues, 1 model selected  

> delete sel

Drag select of 88 residues  

> select clear

Drag select of 57 residues  

> select clear

Drag select of 78 residues  

> select up

719 atoms, 728 bonds, 89 residues, 1 model selected  

> delete sel

Drag select of 3 residues  

> select up

125 atoms, 126 bonds, 16 residues, 1 model selected  

> delete sel

> select clear

> select #61/A:670

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 2 residues  

> select clear

Drag select of 28 residues  

> fitmap #62 inMap #33.1

Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 4038 atoms  
average map value = 0.007876, steps = 40  
shifted from previous position = 0.0144  
rotated from previous position = 0.0178 degrees  
atoms outside contour = 3169, contour level = 0.014811  
  
Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.49227524 -0.83177636 -0.25654079 286.90681543  
-0.53253090 0.05466159 0.84464368 111.49096886  
-0.68853172 0.55241307 -0.46985516 217.06478146  
Axis -0.48599732 0.71842724 0.49766344  
Axis point 201.81610476 0.00000000 36.65534481  
Rotation angle (degrees) 162.50332601  
Shift along axis 48.68741004  
  

> delete sel

> select clear

> fitmap #61 inMap #33.2

Fit molecule copy of copy of copy of A_fixed_model_2_A.pdb (#61) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 2593 atoms  
average map value = 0.01536, steps = 44  
shifted from previous position = 0.0309  
rotated from previous position = 0.286 degrees  
atoms outside contour = 1295, contour level = 0.014809  
  
Position of copy of copy of copy of A_fixed_model_2_A.pdb (#61) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.31750805 -0.91177971 -0.26047341 270.11347052  
-0.60893731 -0.01451577 0.79308552 127.53984411  
-0.72690026 0.41042302 -0.55060781 232.93839308  
Axis -0.56686193 0.69094730 0.44861941  
Axis point 214.45195639 0.00000000 38.26217280  
Rotation angle (degrees) 160.27371795  
Shift along axis 39.50695274  
  

> show #!33 models

> hide #!33 models

> hide #!61 models

> show #!61 models

Drag select of 8 residues  

> select up

138 atoms, 140 bonds, 17 residues, 1 model selected  

> select clear

Drag select of 19 residues  

> select up

196 atoms, 200 bonds, 25 residues, 1 model selected  

> select clear

Drag select of 3 residues  

> select up

41 atoms, 42 bonds, 5 residues, 1 model selected  

> delete sel

> select #61/A:637

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete sel

Drag select of 2 residues  

> delete sel

Drag select of 9 residues  

> delete sel

> select #61/A:625

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #61/A:624

6 atoms, 5 bonds, 1 residue, 1 model selected  

> delete sel

> select #61/A:623

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

[Repeated 1 time(s)]

> select #61/A:622

4 atoms, 3 bonds, 1 residue, 1 model selected  

> delete sel

> fitmap #61 inMap #33.2

Fit molecule copy of copy of copy of A_fixed_model_2_A.pdb (#61) to map
W20_J160_run_ct6_body002.mrc (#33.2) using 2426 atoms  
average map value = 0.01573, steps = 64  
shifted from previous position = 0.0485  
rotated from previous position = 0.404 degrees  
atoms outside contour = 1173, contour level = 0.014809  
  
Position of copy of copy of copy of A_fixed_model_2_A.pdb (#61) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.31268611 -0.91441000 -0.25706370 269.24111705  
-0.61103650 -0.01356040 0.79148626 127.91459578  
-0.72722884 0.40456206 -0.55449774 233.52795858  
Axis -0.56875957 0.69111966 0.44594414  
Axis point 214.64229202 0.00000000 38.50676211  
Rotation angle (degrees) 160.11414397  
Shift along axis 39.41125523  
  

> show #!33 models

> show #!62 models

> hide #!62 models

> show #!60 models

> hide #!61 models

> hide #!60 models

> show #!62 models

> hide #!33 models

Drag select of 2 residues  

> select up

60 atoms, 60 bonds, 7 residues, 1 model selected  

> select up

4038 atoms, 4115 bonds, 507 residues, 1 model selected  

> select down

60 atoms, 60 bonds, 7 residues, 1 model selected  

> select clear

Drag select of 245 residues  

> select up

2197 atoms, 2238 bonds, 276 residues, 1 model selected  

> delete sel

Drag select of 6 residues, 2 pseudobonds  

> select clear

Drag select of 4 residues  

> select up

1841 atoms, 1872 bonds, 231 residues, 1 model selected  

> select down

36 atoms, 4 residues, 1 model selected  

> delete sel

Drag select of 6 residues  

> delete sel

Drag select of 12 residues  

> select up

116 atoms, 117 bonds, 13 residues, 1 model selected  

> delete sel

> select clear

[Repeated 2 time(s)]

> select #62/A:618

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> select #62/A:619

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> select #62/A:620

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #62/A:621

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete sel

> fitmap #62 inMap #33.1

Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 1612 atoms  
average map value = 0.01422, steps = 100  
shifted from previous position = 1.05  
rotated from previous position = 7.03 degrees  
atoms outside contour = 871, contour level = 0.014811  
  
Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.56465803 -0.76120461 -0.31894961 292.13379963  
-0.55687251 0.06616556 0.82795841 113.21112709  
-0.60914228 0.64512763 -0.46125484 203.93497656  
Axis -0.45795004 0.72686749 0.51180603  
Axis point 193.99705310 0.00000000 40.16949466  
Rotation angle (degrees) 168.48533814  
Shift along axis 52.88195186  
  

> show #!33 models

> show #!61 models

> show #!60 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

——— End of log from Fri Jul 4 09:53:55 2025 ———

opened ChimeraX session  

> hide #!33 models

> show #!33 models

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_overall_best_map.ccp4

Opened PredictAndBuild_1_overall_best_map.ccp4 as #63, grid size 138,147,182,
pixel 1.2, shown at level 0.422, step 1, values float32  

> select add #63

2 models selected  

> select subtract #63

Nothing selected  

> hide #!33 models

> volume #63 level 0.2752

> toolshed show

Downloading bundle ChimeraX_locscalesurfer-0.1.1-py3-none-any.whl  
Downloading bundle ChimeraX_ISOLDE-1.9-cp311-cp311-macosx_10_13_universal2.whl  
[Repeated 1 time(s)]

> select add #63

2 models selected  

> show #!1 models

> ui mousemode right "rotate selected models"

> view matrix models
> #63,-0.58537,-0.79697,-0.1489,345.68,-0.68073,0.38338,0.6242,89.496,-0.44039,0.46675,-0.76694,243.81

> fitmap #63 inMap #33.2

Fit map PredictAndBuild_1_overall_best_map.ccp4 in map
W20_J160_run_ct6_body002.mrc using 134378 points  
correlation = 0.4, correlation about mean = 0.0294, overlap = 163.4  
steps = 156, shift = 19.7, angle = 10.1 degrees  
  
Position of PredictAndBuild_1_overall_best_map.ccp4 (#63) relative to
W20_J160_run_ct6_body002.mrc (#33.2) coordinates:  
Matrix rotation and translation  
-0.49730946 -0.85158343 -0.16579799 356.32016493  
-0.56399341 0.17211906 0.80764255 80.81400003  
-0.65923801 0.49515725 -0.56588387 229.61138609  
Axis -0.47998711 0.75793917 0.44174720  
Axis point 229.49905252 0.00000000 52.36918700  
Rotation angle (degrees) 161.00326601  
Shift along axis -8.34680262  
  

> fitmap #63 inMap #2

Fit map PredictAndBuild_1_overall_best_map.ccp4 in map
W20_J3623_consensus_structure.mrc using 134378 points  
correlation = 0.9819, correlation about mean = 0.7973, overlap = 2.007e+04  
steps = 112, shift = 10.7, angle = 7.31 degrees  
  
Position of PredictAndBuild_1_overall_best_map.ccp4 (#63) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.34010494 -0.91904138 -0.19922745 353.84532994  
-0.77653019 0.15497541 0.61072375 146.03986464  
-0.53040504 0.36241629 -0.76637128 277.65026005  
Axis -0.56720681 0.75650641 0.32553722  
Axis point 251.99725576 0.00000000 81.48732765  
Rotation angle (degrees) 167.35637881  
Shift along axis 0.16210555  
  

> select subtract #63

Nothing selected  

> hide #!1 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!63 models

> show #!63 models

> hide #!11 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!63 models

> show #!63 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> close #63

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_overall_best_superposed_predicted_models.pdb

Chain information for
PredictAndBuild_1_overall_best_superposed_predicted_models.pdb #63  
---  
Chain | Description  
A | No description available  
B | No description available  
F | No description available  
  
Computing secondary structure  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_overall_best.pdb

Chain information for PredictAndBuild_1_overall_best.pdb #64  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
F | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_1/PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb

Chain information for
PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb #65  
---  
Chain | Description  
A | No description available  
B | No description available  
F | No description available  
  
Computing secondary structure  

> select add #63

13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected  

> select add #64

34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected  

> select add #65

52865 atoms, 53866 bonds, 30 pseudobonds, 6628 residues, 5 models selected  

> hide sel atoms

> show sel cartoons

Computing secondary structure  

> select subtract #65

34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected  

> select subtract #64

13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected  

> select subtract #63

Nothing selected  

> select add #63

13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected  

> select add #64

34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected  

> select add #65

52865 atoms, 53866 bonds, 30 pseudobonds, 6628 residues, 5 models selected  

> view matrix models
> #63,-0.079462,-0.96928,-0.23276,330.08,-0.99279,0.055943,0.10597,250.15,-0.089693,0.2395,-0.96674,313.02,#64,-0.079462,-0.96928,-0.23276,330.08,-0.99279,0.055943,0.10597,250.15,-0.089693,0.2395,-0.96674,313.02,#65,-0.079462,-0.96928,-0.23276,330.08,-0.99279,0.055943,0.10597,250.15,-0.089693,0.2395,-0.96674,313.02

> ui mousemode right "translate selected models"

> view matrix models
> #63,-0.079462,-0.96928,-0.23276,336.58,-0.99279,0.055943,0.10597,275.32,-0.089693,0.2395,-0.96674,259.8,#64,-0.079462,-0.96928,-0.23276,336.58,-0.99279,0.055943,0.10597,275.32,-0.089693,0.2395,-0.96674,259.8,#65,-0.079462,-0.96928,-0.23276,336.58,-0.99279,0.055943,0.10597,275.32,-0.089693,0.2395,-0.96674,259.8

> view matrix models
> #63,-0.079462,-0.96928,-0.23276,335,-0.99279,0.055943,0.10597,254.69,-0.089693,0.2395,-0.96674,251.24,#64,-0.079462,-0.96928,-0.23276,335,-0.99279,0.055943,0.10597,254.69,-0.089693,0.2395,-0.96674,251.24,#65,-0.079462,-0.96928,-0.23276,335,-0.99279,0.055943,0.10597,254.69,-0.089693,0.2395,-0.96674,251.24

> ui mousemode right "rotate selected models"

> view matrix models
> #63,-0.095152,-0.88164,0.46222,203.93,-0.95238,0.21575,0.21547,206.02,-0.28969,-0.41971,-0.86019,359.38,#64,-0.095152,-0.88164,0.46222,203.93,-0.95238,0.21575,0.21547,206.02,-0.28969,-0.41971,-0.86019,359.38,#65,-0.095152,-0.88164,0.46222,203.93,-0.95238,0.21575,0.21547,206.02,-0.28969,-0.41971,-0.86019,359.38

> ui mousemode right "translate selected models"

> view matrix models
> #63,-0.095152,-0.88164,0.46222,227.08,-0.95238,0.21575,0.21547,215.24,-0.28969,-0.41971,-0.86019,381.48,#64,-0.095152,-0.88164,0.46222,227.08,-0.95238,0.21575,0.21547,215.24,-0.28969,-0.41971,-0.86019,381.48,#65,-0.095152,-0.88164,0.46222,227.08,-0.95238,0.21575,0.21547,215.24,-0.28969,-0.41971,-0.86019,381.48

> hide #!7 models

> show #!33 models

> select subtract #65

34205 atoms, 34848 bonds, 30 pseudobonds, 4274 residues, 4 models selected  

> select subtract #64

13443 atoms, 13688 bonds, 16 pseudobonds, 1678 residues, 2 models selected  

> select subtract #63

Nothing selected  

> hide #65 models

> hide #!64 models

> fitmap #63 inMap #2

Fit molecule PredictAndBuild_1_overall_best_superposed_predicted_models.pdb
(#63) to map W20_J3623_consensus_structure.mrc (#2) using 13443 atoms  
average map value = 0.3311, steps = 268  
shifted from previous position = 24.1  
rotated from previous position = 48.9 degrees  
atoms outside contour = 4479, contour level = 0.25746  
  
Position of PredictAndBuild_1_overall_best_superposed_predicted_models.pdb
(#63) relative to W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.33968216 -0.91923759 -0.19904344 353.65205126  
-0.77596080 0.15430364 0.61161690 145.90271071  
-0.53150812 0.36220526 -0.76570653 277.79017130  
Axis -0.56733253 0.75625188 0.32590934  
Axis point 251.98315191 0.00000000 81.43051773  
Rotation angle (degrees) 167.30207874  
Shift along axis 0.23529698  
  

> hide #!61 models

> hide #!62 models

> hide #!60 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!64 models

> fitmap #64 inMap #2

Fit molecule PredictAndBuild_1_overall_best.pdb (#64) to map
W20_J3623_consensus_structure.mrc (#2) using 20762 atoms  
average map value = 0.2661, steps = 552  
shifted from previous position = 15.4  
rotated from previous position = 48.8 degrees  
atoms outside contour = 10565, contour level = 0.25746  
  
Position of PredictAndBuild_1_overall_best.pdb (#64) relative to
W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.33968228 -0.91946019 -0.19801243 353.57410808  
-0.77672233 0.15550766 0.61034400 145.97075470  
-0.53039456 0.36112372 -0.76698845 277.98078879  
Axis -0.56734428 0.75666030 0.32493947  
Axis point 251.92912923 0.00000000 81.66482425  
Rotation angle (degrees) 167.31225097  
Shift along axis 0.17895697  
  

> hide #!64 models

> show #65 models

> fitmap #65 inMap #2

Fit molecule PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb
(#65) to map W20_J3623_consensus_structure.mrc (#2) using 18660 atoms  
average map value = 0.2436, steps = 340  
shifted from previous position = 22.1  
rotated from previous position = 48.8 degrees  
atoms outside contour = 9859, contour level = 0.25746  
  
Position of PredictAndBuild_1_superposed_predicted_untrimmed_cycle_1.pdb (#65)
relative to W20_J3623_consensus_structure.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.34475277 -0.91893726 -0.19157204 353.38290459  
-0.77178767 0.16132165 0.61507653 143.76727401  
-0.53431202 0.35990227 -0.76484053 278.30475415  
Axis -0.56463658 0.75839755 0.32560511  
Axis point 251.20855212 0.00000000 81.61803612  
Rotation angle (degrees) 166.94047161  
Shift along axis 0.11728580  
  

> hide #65 models

Downloading bundle ChimeraX_ISOLDE-1.9-cp311-cp311-macosx_10_13_universal2.whl  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

——— End of log from Fri Jul 4 10:54:24 2025 ———

opened ChimeraX session  

> show #!46 models

> hide #!46 models

> hide #!50 models

> show #!50 models

> show #!60 models

> hide #!60 models

> show #!60 models

> show #!61 models

> hide #!61 models

> show #!61 models

> show #!62 models

> color #60 #61 #62 navy

> hide #!62 models

> hide #!61 models

> hide #!60 models

> show #!60 models

> show #!61 models

> show #!62 models

> close #57

> close #58

> close #59

> show #51 models

> hide #51 models

> close #51

> show #52 models

> hide #!62 models

> hide #!61 models

> hide #!60 models

> hide #!33 models

> show #35 models

> hide #35 models

> combine #52

> hide #52 models

> ui mousemode right select

> select clear

> select #51/B:953

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

54 atoms, 53 bonds, 7 residues, 1 model selected  

> select up

7500 atoms, 7618 bonds, 953 residues, 1 model selected  

> select down

54 atoms, 53 bonds, 7 residues, 1 model selected  

> select clear

Drag select of 76 residues  

> select up

756 atoms, 763 bonds, 99 residues, 1 model selected  

> select clear

Drag select of 58 residues  

> select up

773 atoms, 785 bonds, 99 residues, 1 model selected  

> delete sel

Drag select of 7 residues  

> delete sel

> select clear

Drag select of 10 residues, 2 pseudobonds  

> select up

110 atoms, 109 bonds, 2 pseudobonds, 15 residues, 2 models selected  

> delete sel

Drag select of 62 residues  

> select up

883 atoms, 897 bonds, 115 residues, 1 model selected  

> delete sel

Drag select of 24 residues, 1 pseudobonds  

> delete sel

Drag select of 2 residues  

> delete sel

> show #!33 models

> hide #!33 models

Drag select of 13 residues  

> select up

126 atoms, 126 bonds, 17 residues, 1 model selected  

> delete sel

Drag select of 7 residues  

> select up

69 atoms, 69 bonds, 9 residues, 1 model selected  

> delete sel

> show #!33 models

> select #51/B:664

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

215 atoms, 217 bonds, 27 residues, 1 model selected  

> delete sel

> select clear

> select #51/B:521

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

334 atoms, 338 bonds, 44 residues, 1 model selected  

> delete sel

> fitmap #51 inMap #33.1

Fit molecule copy of B_fixed_model_2_B.pdb (#51) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 4745 atoms  
average map value = 0.01558, steps = 60  
shifted from previous position = 0.386  
rotated from previous position = 0.444 degrees  
atoms outside contour = 2213, contour level = 0.014811  
  
Position of copy of B_fixed_model_2_B.pdb (#51) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.39489665 -0.88949565 -0.22990026 277.26110723  
-0.63858809 0.08584769 0.76474533 131.14250865  
-0.66050124 0.44880693 -0.60192230 226.00577301  
Axis -0.53542046 0.72973902 0.42521276  
Axis point 208.19952618 0.00000000 43.73317487  
Rotation angle (degrees) 162.84020444  
Shift along axis 43.34907536  
  

> hide #!51 models

> show #52 models

> hide #!50 models

> show #!50 models

> hide #!33 models

Drag select of 161 residues  

> select up

1472 atoms, 1497 bonds, 183 residues, 1 model selected  

> delete sel

Drag select of 68 residues, 3 pseudobonds  

> select clear

Drag select of 90 residues, 3 pseudobonds  

> select up

934 atoms, 946 bonds, 3 pseudobonds, 118 residues, 2 models selected  

> delete sel

Drag select of 208 residues  

> select up

2197 atoms, 2217 bonds, 276 residues, 1 model selected  

> delete sel

Drag select of 109 residues, 2 pseudobonds  

> select clear

Drag select of 98 residues, 2 pseudobonds  

> select clear

> select #52/B:624

6 atoms, 5 bonds, 1 residue, 1 model selected  
Drag select of 109 residues, 2 pseudobonds  

> select up

854 atoms, 863 bonds, 2 pseudobonds, 110 residues, 2 models selected  

> select down

844 atoms, 2 pseudobonds, 109 residues, 2 models selected  

> select clear

Drag select of 109 residues, 2 pseudobonds  

> select up

854 atoms, 863 bonds, 2 pseudobonds, 110 residues, 2 models selected  

> delete sel

> show #!33 models

> show #!37 models

> hide #!37 models

> show #!37 models

> hide #!37 models

> hide #!33 models

Drag select of 3 residues  

> select up

69 atoms, 69 bonds, 9 residues, 1 model selected  

> delete sel

Drag select of 1 residues  

> select clear

[Repeated 1 time(s)]Drag select of 2 residues  

> select up

98 atoms, 98 bonds, 13 residues, 1 model selected  

> select down

12 atoms, 2 residues, 1 model selected  

> select up

98 atoms, 98 bonds, 13 residues, 1 model selected  

> delete sel

> show #!33 models

> fitmap #62 inMap #33.1

Fit molecule copy of copy of A_fixed_model_2_A.pdb (#62) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 1612 atoms  
average map value = 0.01422, steps = 44  
shifted from previous position = 0.0171  
rotated from previous position = 0.0202 degrees  
atoms outside contour = 870, contour level = 0.014811  
  
Position of copy of copy of A_fixed_model_2_A.pdb (#62) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.56449972 -0.76141548 -0.31872643 292.10636189  
-0.55678517 0.06618546 0.82801555 113.19196963  
-0.60936880 0.64487670 -0.46130652 203.97357809  
Axis -0.45800977 0.72686404 0.51175748  
Axis point 194.00483060 0.00000000 40.16620251  
Rotation angle (degrees) 168.46719367  
Shift along axis 52.87260780  
  

> fitmap #52 inMap #33.1

Fit molecule B_fixed_model_2_B.pdb (#52) to map W20_J160_run_ct6_body001.mrc
(#33.1) using 1876 atoms  
average map value = 0.01465, steps = 68  
shifted from previous position = 1.95  
rotated from previous position = 6.84 degrees  
atoms outside contour = 924, contour level = 0.014811  
  
Position of B_fixed_model_2_B.pdb (#52) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.32428809 -0.92759140 -0.18550319 265.85498427  
-0.58447784 0.04228657 0.81030704 122.87471915  
-0.74378954 0.37119543 -0.55586965 237.11232737  
Axis -0.55667228 0.70775295 0.43497325  
Axis point 213.01982007 0.00000000 38.79142480  
Rotation angle (degrees) 156.77096429  
Shift along axis 42.10836361  
  

> show #!51 models

> show #!60 models

> show #!61 models

> show #!62 models

> hide #!62 models

> hide #!61 models

> hide #!60 models

> color #52 betav3

> color #53 betav3

> color #52 betav3

> color #52 betav1

> color #51 betav1

> show #!62 models

> show #!61 models

> show #!60 models

> hide #!52 models

> hide #!51 models

> show #!53 models

> color #53 betapv3

> hide #!53 models

> show #50.1 models

> hide #50.1 models

> show #!50.2 models

> hide #!50.2 models

> show #!50.2 models

> hide #!50.2 models

> show #!50.3 models

> hide #!50.3 models

> show #!50.4 models

> hide #!50.4 models

> show #!50.5 models

> hide #!50.5 models

> show #50.6 models

> show #!50.7 models

> show #36 models

> hide #36 models

> show #36 models

> ui tool show Matchmaker

> matchmaker #50.6#!50.7 to #36

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CopBprime_O55029.pdb, chain A (#36) with
W20_C1_initial_model_no_wat_lig.pdb A5, chain A5 (#50.6), sequence alignment
score = 1599.3  
RMSD between 300 pruned atom pairs is 0.001 angstroms; (across all 300 pairs:
0.001)  
  
Matchmaker CopBprime_O55029.pdb, chain A (#36) with
W20_C1_initial_model_no_wat_lig.pdb A6, chain A6 (#50.7), sequence alignment
score = 2777.6  
RMSD between 535 pruned atom pairs is 0.000 angstroms; (across all 535 pairs:
0.000)  
  

> hide #!60 models

> hide #!61 models

> hide #!62 models

> hide #!33 models

> show #!33 models

> show #!29 models

> hide #!33 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!7 models

> hide #!7 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!13 models

> hide #!13 models

> show #!29 models

> hide #!29 models

> show #!30 models

> hide #!30 models

> show #!31 models

> hide #!31 models

> show #!29 models

> color #29 silver models

> color #29 #c0c0c0bb models

> fitmap #36 inMap #29.1

Fit molecule CopBprime_O55029.pdb (#36) to map W20_J140_run_body001.mrc
(#29.1) using 7214 atoms  
average map value = 0.004094, steps = 196  
shifted from previous position = 6.85  
rotated from previous position = 8.52 degrees  
atoms outside contour = 6338, contour level = 0.01322  
  
Position of CopBprime_O55029.pdb (#36) relative to W20_J140_run_body001.mrc
(#29.1) coordinates:  
Matrix rotation and translation  
0.34093560 0.24287995 0.90816972 145.36424309  
0.84442936 0.34545023 -0.40939370 186.54646641  
-0.41316096 0.90646206 -0.08731868 180.11258285  
Axis 0.67156017 0.67435435 0.30700677  
Axis point 37.00439488 0.00000000 72.89161043  
Rotation angle (degrees) 101.56423540  
Shift along axis 278.71503775  
  

> fitmap #50.7 inMap #29.1

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) to map
W20_J140_run_body001.mrc (#29.1) using 4264 atoms  
average map value = 0.006635, steps = 664  
shifted from previous position = 6.45  
rotated from previous position = 16.7 degrees  
atoms outside contour = 3295, contour level = 0.01322  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A6 (#50.7) relative to
W20_J140_run_body001.mrc (#29.1) coordinates:  
Matrix rotation and translation  
-0.98916440 0.14663035 -0.00730224 336.07347063  
-0.09208236 -0.65838724 -0.74702549 537.00653368  
-0.11434431 -0.73825862 0.66475529 165.63484820  
Axis 0.03349195 0.40893115 -0.91195044  
Axis point 189.25291418 293.62591224 0.00000000  
Rotation angle (degrees) 172.47953493  
Shift along axis 79.80368535  
  

> fitmap #50.6 inMap #29.4

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A5 (#50.6) to map
W20_J140_run_body004.mrc (#29.4) using 2406 atoms  
average map value = 0.01284, steps = 124  
shifted from previous position = 5.65  
rotated from previous position = 34.4 degrees  
atoms outside contour = 1273, contour level = 0.012962  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A5 (#50.6) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
-0.88088930 -0.47324067 0.00879232 419.53745111  
0.15156939 -0.29963122 -0.94193835 456.11372933  
0.44839799 -0.82841077 0.33567073 130.22033922  
Axis 0.14698922 -0.56917708 0.80896948  
Axis point 147.85180587 327.64605342 0.00000000  
Rotation angle (degrees) 157.28319935  
Shift along axis -92.59771834  
  

> hide #36 models

> show #36 models

> hide #36 models

> hide #50.6 models

> show #50.6 models

> hide #50.6 models

> hide #!29 models

> show #50.6 models

> show #36 models

> hide #!50.7 models

> hide #36 models

> show #36 models

> show #!53 models

> hide #!53 models

> close #53

> show #!63 models

> hide #!63 models

> close #63

> close #64

> close #65

> show #!50.7 models

> combine #36

[Repeated 1 time(s)]

> combine #50.7

> hide #!58 models

> hide #!50.7 models

> hide #57 models

> hide #53 models

> hide #36 models

> show #!50.7 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!50.7 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> combine #50.7

> hide #!59 models

> show #!58 models

> hide #50.6 models

Drag select of 156 residues  

> select up

1543 atoms, 1574 bonds, 191 residues, 1 model selected  

> delete sel

Drag select of 37 residues, 1 pseudobonds  

> select up

516 atoms, 519 bonds, 1 pseudobond, 65 residues, 2 models selected  

> delete sel

Drag select of 7 residues, 1 pseudobonds  

> select clear

Drag select of 6 residues, 1 pseudobonds  

> select up

54 atoms, 51 bonds, 1 pseudobond, 9 residues, 2 models selected  

> delete sel

Drag select of 7 residues, 2 pseudobonds  

> select up

93 atoms, 93 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> delete sel

Drag select of 4 residues  

> delete sel

> show #!29 models

> fitmap #58 inMap #29.1

Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#58) to map
W20_J140_run_body001.mrc (#29.1) using 2026 atoms  
average map value = 0.01347, steps = 40  
shifted from previous position = 0.0954  
rotated from previous position = 0.431 degrees  
atoms outside contour = 1055, contour level = 0.01322  
  
Position of copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#58) relative to
W20_J140_run_body001.mrc (#29.1) coordinates:  
Matrix rotation and translation  
-0.98886569 0.14811277 -0.01439634 337.90273979  
-0.08759046 -0.65752799 -0.74832136 536.28441247  
-0.12030195 -0.73872833 0.66318013 167.31953501  
Axis 0.03709874 0.40956482 -0.91152638  
Axis point 190.29117406 293.80476850 0.00000000  
Rotation angle (degrees) 172.57141027  
Shift along axis 79.66282889  
  

> show #!60 models

> show #!61 models

> show #!62 models

> hide #!62 models

> hide #!61 models

> hide #!60 models

> hide #!58 models

> hide #!29 models

> show #!59 models

Drag select of 143 residues, 1 pseudobonds  

> select up

1146 atoms, 1169 bonds, 1 pseudobond, 145 residues, 2 models selected  

> delete sel

> hide #!59 models

> show #!58 models

> hide #!58 models

> show #!59 models

Drag select of 51 residues  

> select up

444 atoms, 452 bonds, 55 residues, 1 model selected  

> delete sel

Drag select of 27 residues  

> delete sel

Drag select of 17 residues  

> select up

199 atoms, 201 bonds, 25 residues, 1 model selected  

> delete sel

> select #59/A6:588

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #59/A6:588

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show #!58 models

> show #!29 models

> hide #!29 models

> hide #!58 models

> delete sel

> select #59/A6:587

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> show #!58 models

> fitmap #59 inMap #29.4

Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#59) to map
W20_J140_run_body004.mrc (#29.4) using 2238 atoms  
average map value = 0.01488, steps = 128  
shifted from previous position = 9.04  
rotated from previous position = 24.7 degrees  
atoms outside contour = 1046, contour level = 0.012962  
  
Position of copy of W20_C1_initial_model_no_wat_lig.pdb A6 (#59) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
-0.85413410 0.51616797 -0.06344729 245.49771496  
-0.20546679 -0.44701353 -0.87061031 558.08387697  
-0.47774295 -0.73058164 0.48786487 300.68201418  
Axis 0.16594922 0.49098549 -0.85521582  
Axis point 220.46254144 334.83017754 0.00000000  
Rotation angle (degrees) 155.04526429  
Shift along axis 57.60322791  
  

> show #!29 models

> show #50.6 models

> hide #!59 models

> hide #!58 models

> show #53 models

> select #29.2

2 models selected  

> select #29.2

2 models selected  

> select clear

[Repeated 1 time(s)]

> select #53/A:876

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

519 atoms, 525 bonds, 67 residues, 1 model selected  

> delete sel

> show #!58 models

> hide #!58 models

> select clear

> select #53/A:640

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide #!29 models

Drag select of 184 residues  

> select up

1682 atoms, 1717 bonds, 208 residues, 1 model selected  

> delete sel

> hide #50.6 models

Drag select of 419 residues, 4 pseudobonds  

> select up

3440 atoms, 3516 bonds, 4 pseudobonds, 432 residues, 2 models selected  

> delete sel

> fitmap #53 inMap #29.1

Fit molecule copy of CopBprime_O55029.pdb (#53) to map
W20_J140_run_body001.mrc (#29.1) using 1573 atoms  
average map value = 0.0152, steps = 92  
shifted from previous position = 4.75  
rotated from previous position = 20.8 degrees  
atoms outside contour = 682, contour level = 0.01322  
  
Position of copy of CopBprime_O55029.pdb (#53) relative to
W20_J140_run_body001.mrc (#29.1) coordinates:  
Matrix rotation and translation  
0.22399917 0.35238232 0.90865344 142.70226714  
0.67056970 0.62083889 -0.40607308 181.66322382  
-0.70722037 0.70027550 -0.09722951 169.81132058  
Axis 0.55763236 0.81444812 0.16037584  
Axis point 78.89411363 0.00000000 66.67498198  
Rotation angle (degrees) 97.24981271  
Shift along axis 254.76430584  
  

> show #!29 models

> hide #!53 models

> show #!53 models

> show #!58 models

> hide #!58 models

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!53 models

> show #57 models

> hide #57 models

> hide #!29 models

> hide #!53 models

> show #57 models

Drag select of 6 residues  

> select up

519 atoms, 525 bonds, 67 residues, 1 model selected  

> delete sel

Drag select of 159 residues  

> select up

1356 atoms, 1383 bonds, 171 residues, 1 model selected  

> delete sel

Drag select of 13 residues, 1 pseudobonds  

> select up

109 atoms, 108 bonds, 1 pseudobond, 14 residues, 2 models selected  

> delete sel

Drag select of 5 residues  

> select clear

Drag select of 8 residues  

> select up

108 atoms, 110 bonds, 13 residues, 1 model selected  

> delete sel

> fitmap #57 inMap #29.4

Fit molecule copy of CopBprime_O55029.pdb (#57) to map
W20_J140_run_body004.mrc (#29.4) using 5122 atoms  
average map value = 0.01184, steps = 144  
shifted from previous position = 8.94  
rotated from previous position = 13.8 degrees  
atoms outside contour = 3092, contour level = 0.012962  
  
Position of copy of CopBprime_O55029.pdb (#57) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
0.19336342 0.06063554 0.97925171 138.80893393  
0.87031534 0.45017771 -0.19972793 186.94884028  
-0.45294790 0.89087786 0.03427586 177.78973972  
Axis 0.55251909 0.72557622 0.41019729  
Axis point 33.82238390 0.00000000 47.06660425  
Rotation angle (degrees) 99.27025680  
Shift along axis 285.26908646  
  

> show #!29 models

> ui tool show "Build Structure"

> toolshed show

> show #!53 models

> hide #!53 models

> fitmap #57 inMap #29.4

Fit molecule copy of CopBprime_O55029.pdb (#57) to map
W20_J140_run_body004.mrc (#29.4) using 5122 atoms  
average map value = 0.01184, steps = 104  
shifted from previous position = 0.0162  
rotated from previous position = 0.0152 degrees  
atoms outside contour = 3088, contour level = 0.012962  
  
Position of copy of CopBprime_O55029.pdb (#57) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
0.19340630 0.06050533 0.97925130 138.80565926  
0.87021654 0.45038133 -0.19969933 186.94266371  
-0.45311938 0.89078379 0.03445385 177.80765427  
Axis 0.55243756 0.72563743 0.41019882  
Axis point 33.85424725 0.00000000 47.07180428  
Rotation angle (degrees) 99.25793540  
Shift along axis 285.27054234  
  

> combine #57

> hide #!29 models

> hide #!63 models

Drag select of 2 residues  

> select up

50 atoms, 50 bonds, 6 residues, 1 model selected  
Drag select of 293 residues  

> select up

2400 atoms, 2461 bonds, 299 residues, 1 model selected  

> delete sel

> fitmap #57 inMap #29.4

Fit molecule copy of CopBprime_O55029.pdb (#57) to map
W20_J140_run_body004.mrc (#29.4) using 2722 atoms  
average map value = 0.01488, steps = 60  
shifted from previous position = 0.588  
rotated from previous position = 4.72 degrees  
atoms outside contour = 1280, contour level = 0.012962  
  
Position of copy of CopBprime_O55029.pdb (#57) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
0.24483069 0.00098871 0.96956534 140.64125601  
0.85587662 0.46963714 -0.21660139 186.15669395  
-0.45555806 0.88285898 0.11413537 178.37372881  
Axis 0.55176004 0.71519280 0.42902227  
Axis point 33.88188669 0.00000000 44.81013344  
Rotation angle (degrees) 94.91618649  
Shift along axis 287.26445575  
  

> show #!29 models

> select add #57

2722 atoms, 2779 bonds, 341 residues, 1 model selected  

> select clear

> select add #57

2722 atoms, 2779 bonds, 341 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #57,0.50755,-0.10762,0.85488,130.21,0.68026,0.65898,-0.32092,190.13,-0.52881,0.74442,0.40768,177.92

> fitmap #57 inMap #29.4

Fit molecule copy of CopBprime_O55029.pdb (#57) to map
W20_J140_run_body004.mrc (#29.4) using 2722 atoms  
average map value = 0.01488, steps = 64  
shifted from previous position = 2.72  
rotated from previous position = 0.042 degrees  
atoms outside contour = 1279, contour level = 0.012962  
  
Position of copy of CopBprime_O55029.pdb (#57) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
0.24476466 0.00100564 0.96958200 140.62777342  
0.85622153 0.46899298 -0.21663398 186.17961813  
-0.45494501 0.88320132 0.11393185 178.36605751  
Axis 0.55197003 0.71492178 0.42920384  
Axis point 33.76576678 0.00000000 44.80708945  
Rotation angle (degrees) 94.94245961  
Shift along axis 287.28157686  
  

> select subtract #57

Nothing selected  

> hide #!57 models

> show #!63 models

> hide #!29 models

> ui mousemode right select

Drag select of 285 residues  

> select up

2450 atoms, 2494 bonds, 306 residues, 1 model selected  

> select up

5122 atoms, 5241 bonds, 640 residues, 1 model selected  

> select clear

Drag select of 338 residues  

> select up

2722 atoms, 2779 bonds, 341 residues, 1 model selected  

> select clear

Drag select of 321 residues  

> select up

2643 atoms, 2694 bonds, 331 residues, 1 model selected  

> select clear

Drag select of 193 residues  

> select up

2186 atoms, 2221 bonds, 272 residues, 1 model selected  

> delete sel

> show #!57 models

> hide #!63 models

> hide #!57 models

> show #!63 models

> select #63/A:10

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #63/A:577

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

219 atoms, 213 bonds, 27 residues, 1 model selected  

> delete sel

> select clear

> select #63/A:430

5 atoms, 4 bonds, 1 residue, 1 model selected  
Drag select of 14 residues, 1 pseudobonds  

> select clear

Drag select of 16 residues, 3 pseudobonds  

> select up

125 atoms, 125 bonds, 3 pseudobonds, 17 residues, 2 models selected  

> delete sel

Drag select of 3 residues  

> delete sel

Drag select of 3 residues  

> select up

42 atoms, 41 bonds, 6 residues, 1 model selected  

> delete sel

> select clear

> select #63/A:353

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

124 atoms, 124 bonds, 16 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]Drag select of 1 residues  

> select down

4 atoms, 1 residue, 1 model selected  

> select up

124 atoms, 124 bonds, 16 residues, 1 model selected  

> select clear

> select #63/A:373

4 atoms, 3 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> select #63/A:354

12 atoms, 12 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> select #63/A:356

9 atoms, 8 bonds, 1 residue, 1 model selected  

> \

Unknown command: \  

> select clear

> select #63/A:355

7 atoms, 7 bonds, 1 residue, 1 model selected  

> \

Unknown command: \  

> delete sel

> select clear

[Repeated 1 time(s)]Drag select of 3 residues, 2 pseudobonds  

> delete sel

> select #63/A:320

6 atoms, 5 bonds, 1 residue, 1 model selected  
Drag select of 1 residues, 2 pseudobonds  

> select up

78 atoms, 76 bonds, 2 pseudobonds, 10 residues, 2 models selected  

> close #63

> combine #36

Drag select of 280 residues  

> select up

3003 atoms, 3050 bonds, 379 residues, 1 model selected  

> delete sel

Drag select of 41 residues, 2 pseudobonds  

> delete sel

Drag select of 122 residues, 3 pseudobonds  

> select up

1221 atoms, 1239 bonds, 3 pseudobonds, 152 residues, 2 models selected  

> delete sel

Drag select of 9 residues, 2 pseudobonds  

> select up

91 atoms, 90 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> delete sel

> select #63/A:373

4 atoms, 3 bonds, 1 residue, 1 model selected  

> delete sel

> select #63/A:356

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> close #63

> show #!53 models

> hide #!53 models

> show #!57 models

> hide #!57 models

> show #50.1 models

> hide #50.1 models

> show #!50.2 models

> hide #!50.2 models

> combine #36

Drag select of 289 residues  

> select up

2306 atoms, 2348 bonds, 291 residues, 1 model selected  

> delete sel

Drag select of 218 residues  

> select up

1888 atoms, 1925 bonds, 237 residues, 1 model selected  

> delete sel

Drag select of 15 residues, 1 pseudobonds  

> select up

152 atoms, 153 bonds, 1 pseudobond, 18 residues, 2 models selected  

> delete sel

Drag select of 4 residues  

> select up

42 atoms, 41 bonds, 5 residues, 1 model selected  

> delete sel

Drag select of 29 residues, 2 pseudobonds  

> select up

302 atoms, 302 bonds, 2 pseudobonds, 39 residues, 2 models selected  

> delete sel

> select clear

[Repeated 1 time(s)]

> select #63/A:305

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

Drag select of 8 residues, 1 pseudobonds  

> select up

119 atoms, 119 bonds, 1 pseudobond, 15 residues, 2 models selected  

> show #!57 models

> delete sel

> fitmap #63 inMap #29.4

Fit molecule copy of CopBprime_O55029.pdb (#63) to map
W20_J140_run_body004.mrc (#29.4) using 2400 atoms  
average map value = 0.01282, steps = 148  
shifted from previous position = 15.9  
rotated from previous position = 27.5 degrees  
atoms outside contour = 1275, contour level = 0.012962  
  
Position of copy of CopBprime_O55029.pdb (#63) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
0.53194142 0.55442248 0.64004222 123.33487031  
0.70035644 0.13679328 -0.70056295 183.98600531  
-0.47596132 0.82091614 -0.31552735 169.31259792  
Axis 0.80394040 0.58968956 0.07711063  
Axis point 0.00000000 -20.96531712 102.68367487  
Rotation angle (degrees) 108.86844509  
Shift along axis 220.70431310  
  

> show #!29 models

> show #!53 models

> show #!58 models

> hide #!58 models

> show #!58 models

> hide #!53 models

> show #!53 models

> hide #!57 models

> show #!57 models

> hide #!57 models

> show #!59 models

> hide #!53 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!57 models

> hide #!57 models

> show #!57 models

> hide #!57 models

> show #!53 models

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!63 models

> hide #!63 models

> show #50.6 models

> show #!63 models

> hide #!63 models

> show #!53 models

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!57 models

> hide #!57 models

> show #!57 models

> hide #!57 models

> combine #57

> hide #!58 models

> hide #!59 models

> hide #50.6 models

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!29 models

> show #50.6 models

> hide #50.6 models

> hide #!63 models

> show #!57 models

> hide #!57 models

> show #!57 models

> hide #!57 models

Drag select of 26 residues  

> select up

229 atoms, 232 bonds, 28 residues, 1 model selected  

> delete sel

Drag select of 9 residues  

> select up

76 atoms, 77 bonds, 10 residues, 1 model selected  

> delete sel

Drag select of 6 residues  

> select clear

Drag select of 10 residues  

> select up

115 atoms, 115 bonds, 14 residues, 1 model selected  

> combine #57

> select add #64

2417 atoms, 2468 bonds, 303 residues, 1 model selected  

> close #64

> hide #!65 models

> show #!65 models

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!57 models

> hide #!57 models

> show #!57 models

> hide #!65 models

Drag select of 31 residues  

> select up

305 atoms, 310 bonds, 38 residues, 1 model selected  

> delete sel

Drag select of 13 residues  

> select up

115 atoms, 115 bonds, 14 residues, 1 model selected  

> delete sel

> hide #!57 models

> show #!53 models

> show #!57 models

> fitmap #57 inMap #29.4

Fit molecule copy of CopBprime_O55029.pdb (#57) to map
W20_J140_run_body004.mrc (#29.4) using 2302 atoms  
average map value = 0.01478, steps = 84  
shifted from previous position = 0.608  
rotated from previous position = 2.11 degrees  
atoms outside contour = 1083, contour level = 0.012962  
  
Position of copy of CopBprime_O55029.pdb (#57) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
0.26430656 -0.02399441 0.96414019 140.91312010  
0.84653335 0.48474763 -0.22000233 186.26213690  
-0.46208585 0.87432489 0.14843404 179.06445534  
Axis 0.54788377 0.71405160 0.43583676  
Axis point 34.54414646 0.00000000 44.00500794  
Rotation angle (degrees) 92.93803311  
Shift along axis 288.24766132  
  

> show #!63 models

> show #!65 models

> hide #!65 models

> show #!65 models

> hide #!65 models

> show #!65 models

> hide #!57 models

> hide #!63 models

Drag select of 243 residues  

> select up

2119 atoms, 2164 bonds, 266 residues, 1 model selected  

> delete sel

> hide #!65 models

> show #!57 models

> show #!63 models

> hide #!63 models

> hide #!57 models

> show #!65 models

Drag select of 17 residues, 1 pseudobonds  

> select up

159 atoms, 159 bonds, 1 pseudobond, 19 residues, 2 models selected  
Drag select of 22 residues, 2 pseudobonds  

> delete sel

> show #!57 models

> select #57/A:547

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> show #!29 models

> hide #!29 models

> hide #!57 models

> select #65/A:588

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> show #!57 models

> fitmap #64 inMap #29.4

No atoms or maps for #64  

> fitmap #65 inMap #29.4

Fit molecule copy of copy of CopBprime_O55029.pdb (#65) to map
W20_J140_run_body004.mrc (#29.4) using 420 atoms  
average map value = 0.02083, steps = 56  
shifted from previous position = 2.51  
rotated from previous position = 13.6 degrees  
atoms outside contour = 145, contour level = 0.012962  
  
Position of copy of copy of CopBprime_O55029.pdb (#65) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
0.25505166 0.23428436 0.93811486 140.41746282  
0.81508493 0.46984578 -0.33894174 184.56399264  
-0.52017805 0.85109094 -0.07112670 178.31682392  
Axis 0.60413780 0.74032411 0.29485206  
Axis point 50.19505778 0.00000000 66.66205089  
Rotation angle (degrees) 99.96896003  
Shift along axis 274.04575231  
  

> show #!29 models

> show #!63 models

> show #!60 models

> show #!61 models

> show #!62 models

> show #!51 models

> show #!52 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

——— End of log from Fri Jul 4 14:29:17 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!65 models

> hide #!63 models

> show #!65 models

> hide #!65 models

> show #!63 models

> show #!65 models

> combine #60 #61 #62

Remapping chain ID 'A' in copy of copy of copy of A_fixed_model_2_A.pdb #61 to
'B'  
Remapping chain ID 'A' in copy of copy of A_fixed_model_2_A.pdb #62 to 'C'  

> rename #64 alpha-COPI

> hide #!64 models

> show #!64 models

> hide #!64 models

> show #!64 models

> hide #!64 models

> hide #!62 models

> hide #!61 models

> hide #!60 models

> show #!64 models

> combine #51 #52

Remapping chain ID 'B' in B_fixed_model_2_B.pdb #52 to 'C'  

> rename #66 beta-COPI

> hide #!66 models

> show #!66 models

> hide #!66 models

> show #!66 models

> hide #!66 models

> hide #!64 models

> show #!64 models

> hide #!52 models

> hide #!51 models

> hide #!65 models

> hide #!63 models

> hide #!57 models

> hide #!53 models

> show #!53 models

> hide #!53 models

> show #!65 models

> hide #!65 models

> show #!63 models

> show #!53 models

> hide #!53 models

> show #!57 models

> show #!53 models

> hide #!53 models

> show #!65 models

> show #!53 models

> combine #63 #57 #65 #53

Remapping chain ID 'A' in copy of CopBprime_O55029.pdb #57 to 'B'  
Remapping chain ID 'A' in copy of copy of CopBprime_O55029.pdb #65 to 'C'  
Remapping chain ID 'A' in copy of CopBprime_O55029.pdb #53 to 'D'  

> rename #67 betaprime-COPI

> hide #!53 models

> hide #!57 models

> hide #!63 models

> hide #!65 models

> show #!66 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

> show #!37 models

> show #!38 models

> hide #!38 models

> hide #!37 models

> show #!50.8 models

> show #50.9 models

> hide #!64 models

> hide #!66 models

> hide #!67 models

> select add #50.9

319 atoms, 320 bonds, 37 residues, 1 model selected  

> fitmap #50.9 inMap #29.4

Fit molecule W20_C1_initial_model_no_wat_lig.pdb A8 (#50.9) to map
W20_J140_run_body004.mrc (#29.4) using 319 atoms  
average map value = 0.01618, steps = 332  
shifted from previous position = 5.67  
rotated from previous position = 32.6 degrees  
atoms outside contour = 181, contour level = 0.012962  
  
Position of W20_C1_initial_model_no_wat_lig.pdb A8 (#50.9) relative to
W20_J140_run_body004.mrc (#29.4) coordinates:  
Matrix rotation and translation  
-0.96507080 0.08189036 0.24886207 278.79886608  
-0.17377809 -0.91094231 -0.37414608 529.42927332  
0.19606003 -0.40432423 0.89335457 -19.89239692  
Axis -0.11483207 0.20091912 -0.97285410  
Axis point 157.88995888 252.84037243 0.00000000  
Rotation angle (degrees) 172.44942844  
Shift along axis 93.70981152  
  

> select subtract #50.9

Nothing selected  

> combine #37

[Repeated 1 time(s)]

> hide #!69 models

> hide #50.9 models

> hide #!29 models

> ui mousemode right select

Drag select of 11 residues  

> select up

319 atoms, 320 bonds, 37 residues, 1 model selected  

> delete sel

> fitmap #68 inMap #29.1

Fit molecule copy of CopD_full_Q5XJY5.pdb (#68) to map
W20_J140_run_body001.mrc (#29.1) using 1112 atoms  
average map value = 0.01419, steps = 64  
shifted from previous position = 0.82  
rotated from previous position = 2.64 degrees  
atoms outside contour = 514, contour level = 0.01322  
  
Position of copy of CopD_full_Q5XJY5.pdb (#68) relative to
W20_J140_run_body001.mrc (#29.1) coordinates:  
Matrix rotation and translation  
-0.11662970 -0.98563516 0.12215086 180.96364645  
-0.16309929 -0.10231295 -0.98129031 185.65988338  
0.97969185 -0.13437031 -0.14882367 140.80476056  
Axis 0.58040695 -0.58768567 0.56369614  
Axis point 145.90273812 0.00000000 210.04228211  
Rotation angle (degrees) 133.14783703  
Shift along axis 75.29400436  
  

> hide #!68 models

> hide #!50.8 models

> show #50.9 models

> show #!69 models

> ui tool show Matchmaker

> matchmaker #!69 to #50.9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A8, chain A8 (#50.9) with copy
of CopD_full_Q5XJY5.pdb, chain A (#69), sequence alignment score = 189.1  
RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
0.000)  
  
Drag select of 135 residues  

> select up

1112 atoms, 1129 bonds, 138 residues, 1 model selected  

> delete sel

> show #!68 models

> hide #50.9 models

> select clear

[Repeated 1 time(s)]

> select #68/A:138

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 6 atom styles  

> hide sel cartoons

> color sel byhetero

> select #69/A:139

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> color sel byhetero

> select clear

> ui tool show "Build Structure"

> select #68/A:138@C

1 atom, 1 residue, 1 model selected  

> select add #69/A:139@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

> undo

Undo failed, probably because structures have been modified.  

> show #!29 models

> build join peptide sel length 1.33 omega 90 phi -120 move small

No chain-terminal carbons in atoms  

> hide #!29 models

Must select exactly 3 atoms in graphics window  

> select #68/A:138@CA

1 atom, 1 residue, 1 model selected  

> select #68/A:138@C

1 atom, 1 residue, 1 model selected  

> select add #68/A:138@CA

2 atoms, 1 residue, 1 model selected  

> select add #68/A:139@N

3 atoms, 2 residues, 1 model selected  
Cannot set the angle if the end atoms have a connection that does not pass
through the center atom  

> select clear

> select #68/A:138@CA

1 atom, 1 residue, 1 model selected  

> select add #68/A:138@C

2 atoms, 1 residue, 1 model selected  

> select add #68/A:139@N

3 atoms, 2 residues, 1 model selected  

> show #!29 models

> angle #68:138@CA@C:139@N 137.7

> angle #68:138@CA@C:139@N 91

> angle #68:138@CA@C:139@N 67.2

> angle #68:138@CA@C:139@N 110.2

> select clear

> select #68/A:152

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

319 atoms, 320 bonds, 37 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> select add #68

1431 atoms, 1450 bonds, 175 residues, 1 model selected  

> select subtract #68

Nothing selected  

> ui mousemode right tug

> ui mousemode right select

> select #68/A:155

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

319 atoms, 320 bonds, 37 residues, 1 model selected  

> ui mousemode right tug

> ui mousemode right "bond rotation"

> ui mousemode right select

> ui mousemode right "play coordinates"

> select add #68

1431 atoms, 1450 bonds, 175 residues, 1 model selected  

> select subtract #68

Nothing selected  

> hide #!68 models

> close #68

> combine 37

Expected a keyword  

> combine #37

> delete sel

> combine #37

> hide #!69 models

> hide #!29 models

> ui mousemode right select

Drag select of 7 residues  

> select up

319 atoms, 320 bonds, 37 residues, 1 model selected  

> combine #37

> delete sel

> close #70

> hide #!68 models

> ui tool show Matchmaker

> matchmaker #!69 to #50.9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A8, chain A8 (#50.9) with copy
of CopD_full_Q5XJY5.pdb, chain A (#69), sequence alignment score = 189.1  
RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
0.000)  
  

> show #!69 models

Drag select of 103 residues  

> select up

936 atoms, 951 bonds, 116 residues, 1 model selected  
Drag select of 135 residues  

> select up

1112 atoms, 1129 bonds, 138 residues, 1 model selected  

> delete sel

> show #!29 models

> show #!68 models

> hide #!29 models

> select #69/A:168

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #69/A:165

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> select #69/A:162

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #69/A:164

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!29 models

> hide #!29 models

> show #!30 models

> select #69/A:165

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> color #30.1 #92929280 models

> color #30.4 #92929263 models

> show #!67 models

> select add #69

319 atoms, 320 bonds, 37 residues, 1 model selected  

> hide sel atoms

> select subtract #69

Nothing selected  

> combine #68 #69

Remapping chain ID 'A' in copy of CopD_full_Q5XJY5.pdb #69 to 'B'  

> rename #70 delta-COPI

> hide #!69 models

> hide #!68 models

> hide #!30.1 models

> show #!30.1 models

> hide #!30 models

> show #!29 models

> show #!66 models

> show #!64 models

> show #39 models

> hide #!29 models

> show #!33 models

> hide #!33 models

> show #!32 models

> hide #!32 models

> show #!33 models

> fitmap #39 inMap #33.3

Fit molecule CopZ1_P61924.pdb (#39) to map W20_J160_run_ct6_body003.mrc
(#33.3) using 1420 atoms  
average map value = 0.0138, steps = 80  
shifted from previous position = 0.00922  
rotated from previous position = 0.0243 degrees  
atoms outside contour = 767, contour level = 0.015167  
  
Position of CopZ1_P61924.pdb (#39) relative to W20_J160_run_ct6_body003.mrc
(#33.3) coordinates:  
Matrix rotation and translation  
-0.59905768 0.35670401 0.71686272 128.55067540  
0.33940715 -0.69775395 0.63082663 127.78309606  
0.72521218 0.62120986 0.29692697 93.14263724  
Axis -0.44771433 -0.38871406 -0.80526596  
Axis point 38.57235221 41.25427436 0.00000000  
Rotation angle (degrees) 179.38464020  
Shift along axis -182.22965962  
  

> hide #39 models

> show #39 models

> combine #39

> rename #71 zeta-COPI

> show #56 models

> hide #56 models

> show #!55 models

> hide #!55 models

> show #!38 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"

> hide #!38 models

> show #!50.4 models

> hide #!50.4 models

> show #!50.4 models

> hide #!50.4 models

> show #!50.4 models

> hide #!50.4 models

> show #50.1 models

> show #!50.2 models

> hide #!50.2 models

> show #!50.3 models

> hide #!50.3 models

> show #!50.4 models

> hide #!50.4 models

> show #!50.5 models

> hide #!50.5 models

> show #50.6 models

> hide #50.6 models

> show #!50.7 models

> hide #!50.7 models

> show #!50.8 models

> hide #!50.8 models

> show #50.9 models

> hide #50.9 models

> show #!50.10 models

> select add #50.10

4143 atoms, 4205 bonds, 2 pseudobonds, 528 residues, 2 models selected  
Drag select of 33.3 W20_J160_run_ct6_body003.mrc , 4 residues  

> select add #50.10

4143 atoms, 4205 bonds, 2 pseudobonds, 528 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #33.3,0.99304,0.059881,0.10144,5.194,-0.064889,0.99679,0.046802,13.668,-0.098315,-0.053059,0.99374,40.329,#50.10,-0.92962,0.23756,-0.28172,353.7,-0.021762,-0.79854,-0.60155,498.49,-0.36787,-0.55308,0.74751,143.01

> undo

[Repeated 1 time(s)]

> ui mousemode right select

> select clear

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopG1_ Q9QZE5.pdb"

CopG1_ Q9QZE5.pdb title:  
Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
info...]  
  
Chain information for CopG1_ Q9QZE5.pdb #72  
---  
Chain | Description | UniProt  
A | coatomer subunit γ-1 | COPG1_MOUSE 1-874  
  
Computing secondary structure  

> select add #72

6830 atoms, 6947 bonds, 874 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #72 to #50.10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker W20_C1_initial_model_no_wat_lig.pdb A9, chain A9 (#50.10) with
CopG1_ Q9QZE5.pdb, chain A (#72), sequence alignment score = 2728.3  
RMSD between 527 pruned atom pairs is 0.000 angstroms; (across all 528 pairs:
0.471)  
  

> select subtract #72

Nothing selected  

> hide #!64 models

> hide #!66 models

> hide #!67 models

> hide #!70 models

> hide #71 models

> hide #39 models

> color #72 gammav3

> fitmap #72 inMap #33.3

Fit molecule CopG1_ Q9QZE5.pdb (#72) to map W20_J160_run_ct6_body003.mrc
(#33.3) using 6830 atoms  
average map value = 0.008592, steps = 128  
shifted from previous position = 5.94  
rotated from previous position = 20.6 degrees  
atoms outside contour = 5149, contour level = 0.015167  
  
Position of CopG1_ Q9QZE5.pdb (#72) relative to W20_J160_run_ct6_body003.mrc
(#33.3) coordinates:  
Matrix rotation and translation  
-0.21262269 0.89025762 0.40278153 115.23719127  
-0.39923844 0.29708069 -0.86738211 108.04417936  
-0.89185215 -0.34523099 0.29225897 114.80605117  
Axis 0.27475861 0.68124291 -0.67853946  
Axis point 106.74618671 0.00000000 53.93689380  
Rotation angle (degrees) 108.15818379  
Shift along axis 27.36630527  
  

> hide #!50.10 models

> hide #50.1 models

> hide #72 models

> show #!41 models

> show #40 models

> hide #40 models

> hide #!41 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/alphafold 3
> /fold_20240724_copbdg1z1_try2/fold_20240724_copbdg1z1_try2_model_0.cif"

Chain information for fold_20240724_copbdg1z1_try2_model_0.cif #73  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #73 to #72

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CopG1_ Q9QZE5.pdb, chain A (#72) with
fold_20240724_copbdg1z1_try2_model_0.cif, chain C (#73), sequence alignment
score = 4461  
RMSD between 219 pruned atom pairs is 1.225 angstroms; (across all 874 pairs:
21.353)  
  

> hide #!50 models

> show #!50 models

> hide #!33 models

> select clear

> select #73/B:154

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

319 atoms, 320 bonds, 37 residues, 1 model selected  

> select up

4014 atoms, 4083 bonds, 511 residues, 1 model selected  

> delete sel

> select #73/A:242

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

49 atoms, 49 bonds, 6 residues, 1 model selected  

> select up

7501 atoms, 7619 bonds, 953 residues, 1 model selected  

> delete sel

> fitmap #73 inMap #33.3

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#73) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 8250 atoms  
average map value = 0.008274, steps = 184  
shifted from previous position = 16.4  
rotated from previous position = 27.6 degrees  
atoms outside contour = 6288, contour level = 0.015167  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#73) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
0.89001705 -0.00769161 -0.45586235 140.75280440  
0.39379749 -0.49091643 0.77712585 125.72122596  
-0.22976767 -0.87117271 -0.43389506 123.79108229  
Axis -0.96307771 -0.13210395 0.23458445  
Axis point 0.00000000 97.90843398 46.99023466  
Rotation angle (degrees) 121.15782367  
Shift along axis -123.12469702  
  

> show #!33 models

> show #71 models

> hide #71 models

> show #71 models

> hide #71 models

> show #71 models

> hide #71 models

> hide #!33 models

> select #73/D:47

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

128 atoms, 129 bonds, 15 residues, 1 model selected  

> select up

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> delete sel

> show #!33 models

> fitmap #73 inMap #33.3

Fit molecule fold_20240724_copbdg1z1_try2_model_0.cif (#73) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 6830 atoms  
average map value = 0.007849, steps = 80  
shifted from previous position = 1.21  
rotated from previous position = 2.15 degrees  
atoms outside contour = 5293, contour level = 0.015167  
  
Position of fold_20240724_copbdg1z1_try2_model_0.cif (#73) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
0.89436621 -0.03216667 -0.44617753 141.60252778  
0.36827977 -0.51322863 0.77522022 126.38957440  
-0.25392733 -0.85764892 -0.44716801 122.18980164  
Axis -0.96493218 -0.11360886 0.23664092  
Axis point 0.00000000 98.06597121 46.27860492  
Rotation angle (degrees) 122.20940815  
Shift along axis -122.08070325  
  

> show #35 models

> close #73

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/alphafold 3
> /fold_20240711_copi_golph3/fold_20240711_copi_golph3_model_0.cif"

Chain information for fold_20240711_copi_golph3_model_0.cif #73  
---  
Chain | Description  
A | .  
B C | .  
D | .  
E | .  
F | .  
G | .  
H | .  
I | .  
  

> ui tool show Matchmaker

> matchmaker #73 to #72

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CopG1_ Q9QZE5.pdb, chain A (#72) with
fold_20240711_copi_golph3_model_0.cif, chain H (#73), sequence alignment score
= 3086.5  
RMSD between 216 pruned atom pairs is 1.190 angstroms; (across all 609 pairs:
15.751)  
  

> hide #35,73 atoms

> hide #35,73 cartoons

> show #35,73 cartoons

> hide #35 models

> hide #!33 models

> select #73/C:142

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

59 atoms, 58 bonds, 8 residues, 1 model selected  

> select up

1457 atoms, 1483 bonds, 181 residues, 1 model selected  

> delete sel

> split #73 chains

Split fold_20240711_copi_golph3_model_0.cif (#73) into 8 models  
Chain information for fold_20240711_copi_golph3_model_0.cif A #73.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_20240711_copi_golph3_model_0.cif B #73.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_20240711_copi_golph3_model_0.cif D #73.3  
---  
Chain | Description  
D | No description available  
  
Chain information for fold_20240711_copi_golph3_model_0.cif E #73.4  
---  
Chain | Description  
E | No description available  
  
Chain information for fold_20240711_copi_golph3_model_0.cif F #73.5  
---  
Chain | Description  
F | No description available  
  
Chain information for fold_20240711_copi_golph3_model_0.cif G #73.6  
---  
Chain | Description  
G | No description available  
  
Chain information for fold_20240711_copi_golph3_model_0.cif H #73.7  
---  
Chain | Description  
H | No description available  
  
Chain information for fold_20240711_copi_golph3_model_0.cif I #73.8  
---  
Chain | Description  
I | No description available  
  

> hide #73.1 models

> show #73.1 models

> close #73.1

> hide #!73 models

> show #!73 models

> hide #73.2 models

> show #73.2 models

> close #73.2

> hide #73.3 models

> show #73.3 models

> close #73.3

> hide #73.4 models

> show #73.4 models

> hide #73.5 models

> show #73.5 models

> close #73.5

> close #73.6

> show #!33 models

> close #73.4

> show #!50.10 models

> hide #!50.10 models

> show #50.9 models

> hide #50.9 models

> show #50.9 models

> hide #50.9 models

> show #50.1 models

> hide #50.1 models

> show #71 models

> close #73.8

> combine #73.7

> hide #73.7 models

> hide #!73 models

> hide #71 models

> hide #!33 models

> show #!33 models

> select #74/H:609

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

227 atoms, 230 bonds, 31 residues, 1 model selected  

> delete sel

> select #74/H:564

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

103 atoms, 104 bonds, 13 residues, 1 model selected  

> select up

4525 atoms, 4596 bonds, 578 residues, 1 model selected  

> select clear

> select #74/H:353

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide #!33 models

Drag select of 109 residues  

> select up

939 atoms, 952 bonds, 119 residues, 1 model selected  

> delete sel

Drag select of 27 residues, 2 pseudobonds  

> delete sel

> fitmap #74 inMap #33.3

Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#74) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 3367 atoms  
average map value = 0.01504, steps = 104  
shifted from previous position = 1.23  
rotated from previous position = 8.87 degrees  
atoms outside contour = 1844, contour level = 0.015167  
  
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#74) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
-0.99039171 0.12782412 -0.05277549 148.12639654  
0.13807487 0.93531006 -0.32577664 131.22576391  
0.00771933 -0.32993345 -0.94397263 135.30516062  
Axis -0.06759286 -0.98369069 0.16668480  
Axis point 68.34524384 0.00000000 79.86683576  
Rotation angle (degrees) 178.23793985  
Shift along axis -116.54453594  
  

> show #!33 models

> hide #!33 models

Drag select of 37 residues  

> select up

343 atoms, 348 bonds, 42 residues, 1 model selected  

> delete sel

> fitmap #74 inMap #33.3

Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#74) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 3024 atoms  
average map value = 0.01541, steps = 84  
shifted from previous position = 0.341  
rotated from previous position = 2.61 degrees  
atoms outside contour = 1604, contour level = 0.015167  
  
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#74) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
-0.99016649 0.13961225 -0.00887325 145.93626541  
0.13499683 0.93694534 -0.32234963 131.14942473  
-0.03669021 -0.32037766 -0.94657909 136.23220850  
Axis 0.06976430 0.98410929 -0.16328456  
Axis point 68.87722497 0.00000000 78.50166031  
Rotation angle (degrees) 179.19020792  
Shift along axis 117.00189352  
  

> show #!33 models

> hide #!33 models

Drag select of 7 residues  

> select up

130 atoms, 130 bonds, 17 residues, 1 model selected  
Drag select of 5 residues  

> select down

44 atoms, 5 residues, 1 model selected  

> select up

142 atoms, 143 bonds, 18 residues, 1 model selected  

> delete sel

> fitmap #74 inMap #33.3

Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#74) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 2882 atoms  
average map value = 0.01543, steps = 60  
shifted from previous position = 0.199  
rotated from previous position = 0.43 degrees  
atoms outside contour = 1520, contour level = 0.015167  
  
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#74) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
-0.99012237 0.14014794 -0.00403046 145.70159327  
0.13418777 0.93889954 -0.31695629 130.92767817  
-0.04063657 -0.31436635 -0.94843158 136.20145596  
Axis 0.06966230 0.98460506 -0.16031230  
Axis point 68.95076353 0.00000000 78.11025829  
Rotation angle (degrees) 178.93485378  
Shift along axis 117.22719466  
  

> show #!33 models

> show #!50.10 models

> hide #!50 models

> show #!50 models

> hide #!33 models

> combine #50.10

> hide #!50.10 models

> hide #!74 models

> show #!74 models

> hide #!74 models

Drag select of 113 residues  

> select up

1028 atoms, 1042 bonds, 130 residues, 1 model selected  

> delete sel

> fitmap #75 inMap #33.3

Fit molecule copy of W20_C1_initial_model_no_wat_lig.pdb A9 (#75) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 3115 atoms  
average map value = 0.01389, steps = 132  
shifted from previous position = 1.68  
rotated from previous position = 15.8 degrees  
atoms outside contour = 1847, contour level = 0.015167  
  
Position of copy of W20_C1_initial_model_no_wat_lig.pdb A9 (#75) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
-0.96975860 0.09758407 -0.22370877 404.94223752  
0.05855198 -0.79680528 -0.60139256 482.79146988  
-0.23693866 -0.59630420 0.76699503 131.62487193  
Axis 0.12253380 0.31859145 -0.93993880  
Axis point 213.57688590 261.52023160 0.00000000  
Rotation angle (degrees) 178.81027642  
Shift along axis 79.71302152  
  

> show #!33 models

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Final maps and model/Model_files/20250328_COPI_GOLPH3_model_v2.cif"

Chain information for 20250328_COPI_GOLPH3_model_v2.cif #76  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
R S T | No description available  
  

> hide #76#!75 atoms

> show #76#!75 cartoons

> ui tool show Matchmaker

> matchmaker #76 to #66

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker beta-COPI, chain B (#66) with 20250328_COPI_GOLPH3_model_v2.cif,
chain J (#76), sequence alignment score = 1591  
RMSD between 180 pruned atom pairs is 0.463 angstroms; (across all 289 pairs:
3.827)  
  

> show #!66 models

> hide #!66 models

> show #!66 models

> hide #76 models

> show #76 models

> hide #76 models

> show #76 models

> select add #76

17013 atoms, 16995 bonds, 4252 residues, 1 model selected  

> select subtract #76

Nothing selected  

> hide #76 models

> hide #!75 models

> show #76 models

> select add #76

17013 atoms, 16995 bonds, 4252 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #76,-0.94328,0.33002,0.036298,249.11,-0.21754,-0.53176,-0.81848,562.73,-0.25081,-0.77995,0.57339,257.94

> fitmap #76 inMap #33.1

Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 17013 atoms  
average map value = 0.005784, steps = 248  
shifted from previous position = 23.7  
rotated from previous position = 25.1 degrees  
atoms outside contour = 13846, contour level = 0.014811  
  
Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.95309148 0.15118983 -0.26221799 379.07308450  
0.09927921 -0.66223841 -0.74268696 486.62957335  
-0.28593754 -0.73388141 0.61616378 222.17176604  
Axis 0.15248160 0.41074018 -0.89891149  
Axis point 212.09731096 291.09961203 0.00000000  
Rotation angle (degrees) 178.34540300  
Shift along axis 57.96723338  
  

> select subtract #76

Nothing selected  

> ui tool show Matchmaker

> matchmaker #76 to #66

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker beta-COPI, chain B (#66) with 20250328_COPI_GOLPH3_model_v2.cif,
chain J (#76), sequence alignment score = 1591  
RMSD between 180 pruned atom pairs is 0.463 angstroms; (across all 289 pairs:
3.827)  
  

> undo

> view matrix models
> #76,-0.94328,0.33002,0.036298,269.75,-0.21754,-0.53176,-0.81848,549.29,-0.25081,-0.77995,0.57339,234.77

> select subtract #76

Nothing selected  

> select add #76

17013 atoms, 16995 bonds, 4252 residues, 1 model selected  

> view matrix models
> #76,-0.94328,0.33002,0.036298,244.4,-0.21754,-0.53176,-0.81848,557.07,-0.25081,-0.77995,0.57339,249.76

> show #!51 models

> hide #!51 models

> show #!52 models

> hide #!52 models

> hide #!66 models

> show #!52 models

> hide #!52 models

> show #!51 models

> hide #!51 models

> ui tool show Matchmaker

> matchmaker #76 to #51

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of B_fixed_model_2_B.pdb, chain B (#51) with
20250328_COPI_GOLPH3_model_v2.cif, chain J (#76), sequence alignment score =
1591  
RMSD between 180 pruned atom pairs is 0.463 angstroms; (across all 289 pairs:
3.827)  
  

> view matrix models
> #76,-0.94328,0.33002,0.036298,250.65,-0.21754,-0.53176,-0.81848,564.67,-0.25081,-0.77995,0.57339,248.23

> fitmap #76 inMap #33.1

Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 17013 atoms  
average map value = 0.005784, steps = 256  
shifted from previous position = 20.4  
rotated from previous position = 25.2 degrees  
atoms outside contour = 13847, contour level = 0.014811  
  
Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.95306184 0.15114897 -0.26234924 379.12122640  
0.09940762 -0.66223994 -0.74266842 486.60244827  
-0.28599171 -0.73388844 0.61613026 222.19665492  
Axis 0.15253453 0.41074061 -0.89890231  
Axis point 212.11797169 291.10158267 0.00000000  
Rotation angle (degrees) 178.35078282  
Shift along axis 57.96337940  
  

> select subtract #76

Nothing selected  

> hide #!50 models

> show #!50 models

> hide #!33 models

> ui mousemode right select

> select clear

> select #76/F:486

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 6 residues, 1 model selected  

> select up

2344 atoms, 2343 bonds, 586 residues, 1 model selected  

> select up

17013 atoms, 16995 bonds, 4252 residues, 1 model selected  

> select down

2344 atoms, 2343 bonds, 586 residues, 1 model selected  

> delete sel

> select #76/L:158

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 234 residues  

> select clear

Drag select of 67 residues  

> select up

544 atoms, 538 bonds, 136 residues, 1 model selected  

> select up

1940 atoms, 1938 bonds, 485 residues, 1 model selected  

> delete sel

> select #76/T:111

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

48 atoms, 47 bonds, 12 residues, 1 model selected  

> select up

669 atoms, 668 bonds, 167 residues, 1 model selected  

> delete sel

> select clear

[Repeated 1 time(s)]

> select #76/L:243

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

48 atoms, 47 bonds, 12 residues, 1 model selected  

> select up

804 atoms, 803 bonds, 201 residues, 1 model selected  

> delete sel

> select #76/K:689

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 10 residues, 1 model selected  

> select up

204 atoms, 203 bonds, 51 residues, 1 model selected  

> delete sel

> select clear

> select #76/J:133

4 atoms, 3 bonds, 1 residue, 1 model selected  
Drag select of 60 residues  

> select clear

Drag select of 34 residues  

> select up

204 atoms, 200 bonds, 51 residues, 1 model selected  

> select up

1244 atoms, 1243 bonds, 311 residues, 1 model selected  

> delete sel

> select clear

> select #76/S:91

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

28 atoms, 27 bonds, 7 residues, 1 model selected  

> select up

669 atoms, 668 bonds, 167 residues, 1 model selected  

> delete sel

> select #76/R:138

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

32 atoms, 31 bonds, 8 residues, 1 model selected  

> select up

669 atoms, 668 bonds, 167 residues, 1 model selected  

> delete sel

> select clear

> select #76/H:729

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #76/H:727

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

Drag select of 12 residues  

> select clear

Drag select of 63 residues  

> select up

432 atoms, 427 bonds, 108 residues, 1 model selected  

> select up

3337 atoms, 3335 bonds, 834 residues, 1 model selected  

> delete sel

Drag select of 61 residues  

> select up

509 atoms, 503 bonds, 127 residues, 1 model selected  

> select up

977 atoms, 976 bonds, 244 residues, 1 model selected  

> delete sel

> show #!33 models

> hide #76 models

> show #76 models

> show #!75 models

> hide #!75 models

> show #!74 models

> hide #76 models

> show #76 models

> hide #!74 models

> show #!74 models

> hide #76 models

> hide #!50 models

> show #76 models

> hide #!33 models

> select clear

> select #76/I:400

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

64 atoms, 63 bonds, 16 residues, 1 model selected  

> select up

1252 atoms, 1251 bonds, 313 residues, 1 model selected  

> delete sel

> show #50.9 models

> hide #50.9 models

> show #!50.10 models

> hide #!50.10 models

> show #!50.10 models

> hide #!50.10 models

> show #50.9 models

> hide #50.9 models

> show #!50.8 models

> hide #!50.8 models

> show #72 models

> hide #72 models

> show #72 models

> hide #72 models

> show #!75 models

> hide #!75 models

> hide #76 models

> show #76 models

> hide #!74 models

> show #!75 models

> hide #!75 models

> select #76/A:21

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

36 atoms, 35 bonds, 9 residues, 1 model selected  

> select up

64 atoms, 63 bonds, 16 residues, 1 model selected  

> delete sel

Drag select of 15 residues  

> select up

116 atoms, 112 bonds, 29 residues, 1 model selected  

> select up

580 atoms, 579 bonds, 145 residues, 1 model selected  

> delete sel

> show #!75 models

> hide #!75 models

> show #!74 models

> show #!33 models

> select clear

> select #76/O:107

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

48 atoms, 47 bonds, 12 residues, 1 model selected  

> select up

1132 atoms, 1131 bonds, 283 residues, 1 model selected  

> delete sel

> hide #!33 models

> hide #!74 models

> show #!74 models

> hide #76 models

> hide #!74 models

> show #76 models

> select #76/M:371

4 atoms, 3 bonds, 1 residue, 1 model selected  
Drag select of 16 residues  

> select up

144 atoms, 142 bonds, 36 residues, 1 model selected  
Drag select of 48 residues  

> select up

216 atoms, 215 bonds, 54 residues, 1 model selected  

> delete sel

> show #!74 models

> show #!33 models

> show #!66 models

> hide #76 models

> hide #!66 models

> show #76 models

> hide #!33 models

> show #!33 models

> hide #!33 models

> hide #76 models

> show #!33 models

> show #76 models

> hide #!33 models

> hide #!74 models

> select #76/M:354

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

12 atoms, 11 bonds, 3 residues, 1 model selected  

> select up

380 atoms, 379 bonds, 95 residues, 1 model selected  

> select #76/M:363

4 atoms, 3 bonds, 1 residue, 1 model selected  
Drag select of 8 residues  

> select up

52 atoms, 51 bonds, 13 residues, 1 model selected  

> delete sel

Drag select of 4 residues  

> select clear

Drag select of 5 residues  

> delete sel

> show #!74 models

> show #!33 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments_v2.cxs"

[Repeated 1 time(s)]

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250705_W20_COPI_cyto_alignments.cxs"

——— End of log from Sat Jul 5 20:47:49 2025 ———

> view name session-start

opened ChimeraX session  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_overall_best_superposed_predicted_models.pdb

Chain information for
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb #77  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_overall_best.pdb

Chain information for PredictAndBuild_7_overall_best.pdb #78  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb

Chain information for
PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb #79  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_7/PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb

Chain information for
PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb #80  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
[Repeated 3 time(s)]

> ui tool show Matchmaker

> hide #!74 models

> show #!74 models

> hide #!74 models

> show #!74 models

> matchmaker #78-80#!77 to #74

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
PredictAndBuild_7_overall_best.pdb, chain A (#78), sequence alignment score =
2265.6  
RMSD between 256 pruned atom pairs is 1.119 angstroms; (across all 355 pairs:
2.263)  
  
Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb, chain A (#79),
sequence alignment score = 2735.5  
RMSD between 235 pruned atom pairs is 0.805 angstroms; (across all 372 pairs:
5.897)  
  
Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#80),
sequence alignment score = 2729.5  
RMSD between 327 pruned atom pairs is 0.888 angstroms; (across all 372 pairs:
4.838)  
  
Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#74) with
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb, chain A (#77),
sequence alignment score = 2526.8  
RMSD between 255 pruned atom pairs is 0.833 angstroms; (across all 351 pairs:
2.256)  
  

> hide #!74 models

> hide #76 models

> hide #79 models

> hide #80 models

> hide #78 models

> show #76 models

> hide #76 models

> show #76 models

> hide #76 models

> show #!74 models

> hide #!74 models

> show #!74 models

> hide #!33 models

> show #!33 models

> show #!64 models

> show #!66 models

> color #77 gammav3

> hide #!74 models

> show #76 models

> hide #76 models

> show #76 models

> hide #!77 models

> show #!77 models

> hide #!77 models

> show #!77 models

> hide #!77 models

> show #!77 models

> hide #!33 models

> hide #!64 models

> ui mousemode right select

Drag select of 31 residues  

> select up

390 atoms, 396 bonds, 49 residues, 1 model selected  

> select up

2085 atoms, 2126 bonds, 265 residues, 1 model selected  

> select down

390 atoms, 396 bonds, 49 residues, 1 model selected  

> select up

2085 atoms, 2126 bonds, 265 residues, 1 model selected  

> show #!33 models

> delete sel

> hide #!33 models

> hide #!66 models

> show #78 models

> hide #78 models

> combine #77

[Repeated 1 time(s)]

> hide #!77 models

> hide #!82 models

> hide #76 models

> show #76 models

> show #78 models

> hide #!81 models

> show #!82 models

> hide #!82 models

> show #80 models

> hide #80 models

> hide #78 models

> show #78 models

> hide #78 models

> show #79 models

> show #78 models

> hide #78 models

> hide #79 models

> show #!81 models

Drag select of 111 residues  

> select up

1038 atoms, 1052 bonds, 134 residues, 1 model selected  

> delete sel

Drag select of 57 residues, 2 pseudobonds  

> select clear

Drag select of 53 residues, 2 pseudobonds  

> delete sel

Drag select of 69 residues, 3 pseudobonds  

> select up

582 atoms, 590 bonds, 3 pseudobonds, 73 residues, 2 models selected  

> delete sel

> fitmap #81 inMap 33.3

Invalid "inMap" argument: invalid density map specifier  

> fitmap #81 inMap #33.3

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 2348 atoms  
average map value = 0.0134, steps = 120  
shifted from previous position = 3.48  
rotated from previous position = 4.21 degrees  
atoms outside contour = 1408, contour level = 0.015167  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
to W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
-0.20129859 -0.97948015 -0.00987448 314.24082722  
-0.86511694 0.17304913 0.47077242 170.18293950  
-0.45940347 0.10330841 -0.88219942 322.78012223  
Axis -0.62096341 0.75964188 0.19325802  
Axis point 258.89532999 0.00000000 108.65698241  
Rotation angle (degrees) 162.78955563  
Shift along axis -3.47411885  
  

> show #!33 models

> fitmap #81 inMap #33.1

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 2348 atoms  
average map value = 0.01071, steps = 112  
shifted from previous position = 3.4  
rotated from previous position = 15.1 degrees  
atoms outside contour = 1585, contour level = 0.014811  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
to W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.22739783 -0.93674263 -0.26608921 334.89658150  
-0.70727752 -0.02894807 0.70634306 146.59781389  
-0.66936442 0.34881979 -0.65595428 290.22146917  
Axis -0.61036394 0.68847171 0.39174298  
Axis point 263.55345573 -0.00000000 66.31084802  
Rotation angle (degrees) 162.96971650  
Shift along axis 10.21187265  
  

> hide #!33 models

> select add #81

2348 atoms, 2383 bonds, 301 residues, 1 model selected  
Drag select of 14 residues  

> select add #81

2384 atoms, 2383 bonds, 310 residues, 2 models selected  

> select subtract #81

36 atoms, 9 residues, 1 model selected  

> select add #81

2384 atoms, 2383 bonds, 310 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #76,-0.93321,0.21477,-0.28809,372.34,1.5257e-05,-0.80171,-0.59771,509.2,-0.35934,-0.5578,0.74816,166.22,#81,-0.16626,-0.95754,-0.23551,330.74,-0.84489,0.015188,0.53472,191.15,-0.50844,0.28789,-0.81155,305.14

> view matrix models
> #76,-0.93321,0.21477,-0.28809,369.46,1.5257e-05,-0.80171,-0.59771,509.45,-0.35934,-0.5578,0.74816,167.85,#81,-0.16626,-0.95754,-0.23551,327.86,-0.84489,0.015188,0.53472,191.4,-0.50844,0.28789,-0.81155,306.78

> view matrix models
> #76,-0.93321,0.21477,-0.28809,362.81,1.5257e-05,-0.80171,-0.59771,510.16,-0.35934,-0.5578,0.74816,162.77,#81,-0.16626,-0.95754,-0.23551,321.21,-0.84489,0.015188,0.53472,192.11,-0.50844,0.28789,-0.81155,301.69

> select add #76

3188 atoms, 3221 bonds, 511 residues, 2 models selected  

> show #!33 models

> view matrix models
> #76,-0.93321,0.21477,-0.28809,370.55,1.5257e-05,-0.80171,-0.59771,509.34,-0.35934,-0.5578,0.74816,168.09,#81,-0.16626,-0.95754,-0.23551,328.95,-0.84489,0.015188,0.53472,191.29,-0.50844,0.28789,-0.81155,307.01

> select subtract #81

840 atoms, 838 bonds, 210 residues, 1 model selected  

> fitmap #76 inMap #33.1

Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 840 atoms  
average map value = 0.02202, steps = 60  
shifted from previous position = 2.45  
rotated from previous position = 5.43 degrees  
atoms outside contour = 170, contour level = 0.014811  
  
Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.96070020 0.05782811 -0.27149776 408.93422016  
0.16204598 -0.67727713 -0.71766064 466.60813032  
-0.22538019 -0.73345184 0.64128946 199.29795302  
Axis -0.13724964 -0.40083218 0.90581239  
Axis point 212.55034942 283.76140105 0.00000000  
Rotation angle (degrees) 176.70210838  
Shift along axis -62.63107629  
  

> fitmap #81 inMap #33.1

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 2348 atoms  
average map value = 0.01071, steps = 56  
shifted from previous position = 1.86  
rotated from previous position = 0.0322 degrees  
atoms outside contour = 1584, contour level = 0.014811  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
to W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.22745563 -0.93688214 -0.26554811 334.85796779  
-0.70718029 -0.02854799 0.70645669 146.50571825  
-0.66944752 0.34847794 -0.65605118 290.29252721  
Axis -0.61030750 0.68859628 0.39161196  
Axis point 263.52285147 0.00000000 66.35287841  
Rotation angle (degrees) 162.94573059  
Shift along axis 10.19898967  
  

> hide #!81 models

> hide #76 models

> show #!81 models

> hide #!33 models

> view matrix models
> #76,-0.94628,0.12198,-0.29946,442.05,0.074145,-0.8196,-0.56813,481.51,-0.31474,-0.55981,0.76652,186.98

> ui mousemode right select

Drag select of 123 residues  

> select up

983 atoms, 995 bonds, 129 residues, 1 model selected  

> delete sel

> show #!33 models

> fitmap #81 inMap #33.1

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 1365 atoms  
average map value = 0.01415, steps = 116  
shifted from previous position = 2.3  
rotated from previous position = 16.3 degrees  
atoms outside contour = 753, contour level = 0.014811  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
to W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
0.01747338 -0.99098181 -0.13285229 281.52273337  
-0.71306863 -0.10549261 0.69311214 162.28311421  
-0.70087645 0.08262179 -0.70848136 343.51081858  
Axis -0.69455315 0.64623949 0.31618104  
Axis point 0.00000000 268.41792558 210.72025848  
Rotation angle (degrees) 153.92902085  
Shift along axis 17.95286420  
  

> show #!74 models

> hide #!74 models

> show #!75 models

> hide #!75 models

> show #76 models

> select add #76

840 atoms, 838 bonds, 210 residues, 1 model selected  
Drag select of 33.1 W20_J160_run_ct6_body001.mrc , 2 residues  

> select clear

> select add #76

840 atoms, 838 bonds, 210 residues, 1 model selected  
Drag select of 33.1 W20_J160_run_ct6_body001.mrc , 5 residues  

> select add #76

840 atoms, 838 bonds, 210 residues, 3 models selected  

> select subtract #76

2 models selected  

> select clear

> select add #76

840 atoms, 838 bonds, 210 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #76,-0.94628,0.12198,-0.29946,406.27,0.074145,-0.8196,-0.56813,495.91,-0.31474,-0.55981,0.76652,151.84

> fitmap #76 inMap #33.1

Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 840 atoms  
average map value = 0.02201, steps = 112  
shifted from previous position = 10.6  
rotated from previous position = 0.0236 degrees  
atoms outside contour = 169, contour level = 0.014811  
  
Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
-0.96080554 0.05790187 -0.27110898 408.84449350  
0.16172293 -0.67722645 -0.71778133 466.70494589  
-0.22516305 -0.73349282 0.64131886 199.25734435  
Axis -0.13708008 -0.40087044 0.90582114  
Axis point 212.50907521 283.77894704 0.00000000  
Rotation angle (degrees) 176.71471075  
Shift along axis -62.64113752  
  

> select subtract #76

Nothing selected  

> hide #76 models

> hide #!33 models

> ui mousemode right select

Drag select of 66 residues  

> select up

1365 atoms, 1387 bonds, 172 residues, 1 model selected  

> select down

533 atoms, 66 residues, 1 model selected  

> delete sel

> fitmap #81 inMap #33.1

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 832 atoms  
average map value = 0.01316, steps = 84  
shifted from previous position = 3.31  
rotated from previous position = 11.8 degrees  
atoms outside contour = 498, contour level = 0.014811  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
to W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
0.14691503 -0.96385323 -0.22226771 264.04905282  
-0.78499351 -0.25032946 0.56667482 218.34222261  
-0.60183151 0.09122566 -0.79339568 335.48317698  
Axis -0.74977491 0.59856539 0.28205861  
Axis point 0.00000000 250.13903908 195.48982431  
Rotation angle (degrees) 161.51470465  
Shift along axis 27.34066185  
  

> show #!33 models

> show #76 models

> hide #!33 models

> hide #76 models

Drag select of 75 residues  

> delete sel

> fitmap #81 inMap #33.1

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
W20_J160_run_ct6_body001.mrc (#33.1) using 239 atoms  
average map value = 0.01661, steps = 68  
shifted from previous position = 0.894  
rotated from previous position = 22.1 degrees  
atoms outside contour = 87, contour level = 0.014811  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
to W20_J160_run_ct6_body001.mrc (#33.1) coordinates:  
Matrix rotation and translation  
0.01560880 -0.84592101 -0.53307975 307.86268532  
-0.85667939 -0.28624403 0.42914424 255.66225987  
-0.51561303 0.44998001 -0.72915101 245.26898996  
Axis 0.71258549 -0.59736389 -0.36793789  
Axis point 0.00000000 255.65895561 203.35484992  
Rotation angle (degrees) 179.16231543  
Shift along axis -23.58867527  
  

> show #76 models

> show #!33 models

> hide #!33 models

> show #!82 models

> hide #76 models

> hide #!81 models

Drag select of 9 residues  

> select add #82

4394 atoms, 4464 bonds, 1 pseudobond, 561 residues, 2 models selected  

> select subtract #82

Nothing selected  

> show #!81 models

> hide #!82 models

> hide #!81 models

> show #!74 models

> hide #!74 models

> show #76 models

> show #!77 models

> hide #!77 models

> show #78 models

> show #!33 models

> combine #78

> hide #78 models

> hide #!33 models

> hide #76 models

> show #76 models

> hide #76 models

> show #76 models

> hide #76 models

Drag select of 49 residues  

> select up

441 atoms, 448 bonds, 56 residues, 1 model selected  

> delete sel

> show #!74 models

> hide #!74 models

> show #76 models

> fitmap #83 inMap #33.3

Fit molecule copy of PredictAndBuild_7_overall_best.pdb (#83) to map
W20_J160_run_ct6_body003.mrc (#33.3) using 3367 atoms  
average map value = 0.01915, steps = 88  
shifted from previous position = 1.31  
rotated from previous position = 3.07 degrees  
atoms outside contour = 1342, contour level = 0.015167  
  
Position of copy of PredictAndBuild_7_overall_best.pdb (#83) relative to
W20_J160_run_ct6_body003.mrc (#33.3) coordinates:  
Matrix rotation and translation  
-0.19901990 -0.97974509 -0.02215055 315.72725675  
-0.86258557 0.16440368 0.47845331 170.01428108  
-0.46512065 0.11432847 -0.87783357 321.74102683  
Axis -0.62215321 0.75687028 0.20018181  
Axis point 259.60135583 0.00000000 107.39223084  
Rotation angle (degrees) 162.98435754  
Shift along axis -3.34526606  
  

> show #!33 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250705_W20_COPI_cyto_alignments.cxs"

> hide #!33 models

> show #!9 models

> hide #!9 models

> show #!45 models

> show #!46 models

> hide #!46 models

> hide #!45 models

> show #!23 models

> hide #!23 models

> show #!25 models

> fitmap #76 inMap #25

Fit molecule 20250328_COPI_GOLPH3_model_v2.cif (#76) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 840 atoms  
average map value = 0.4915, steps = 56  
shifted from previous position = 1.01  
rotated from previous position = 4.93 degrees  
atoms outside contour = 19, contour level = 0.2532  
  
Position of 20250328_COPI_GOLPH3_model_v2.cif (#76) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.95361160 0.05892580 -0.29521631 421.68865993  
0.13475176 -0.79337176 -0.59363560 471.58547391  
-0.26919673 -0.60587871 0.74862815 156.24096699  
Axis -0.15097143 -0.32085083 0.93501999  
Axis point 218.58287062 267.06046758 0.00000000  
Rotation angle (degrees) 177.67614662  
Shift along axis -68.88310337  
  

> fitmap #77 inMap #25

Fit molecule PredictAndBuild_7_overall_best_superposed_predicted_models.pdb
(#77) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4394
atoms  
average map value = 0.2705, steps = 120  
shifted from previous position = 6.58  
rotated from previous position = 13.2 degrees  
atoms outside contour = 2142, contour level = 0.2532  
  
Position of PredictAndBuild_7_overall_best_superposed_predicted_models.pdb
(#77) relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25)
coordinates:  
Matrix rotation and translation  
-0.08911154 -0.97740547 -0.19167078 312.61104116  
-0.86513544 -0.01940313 0.50116283 207.38914458  
-0.49355830 0.21048058 -0.84385907 317.01597391  
Axis -0.66998680 0.69581356 0.25876858  
Axis point 280.81289084 0.00000000 94.39286792  
Rotation angle (degrees) 167.47114130  
Shift along axis 16.89268056  
  

> fitmap #78 inMap #25

Fit molecule PredictAndBuild_7_overall_best.pdb (#78) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3808 atoms  
average map value = 0.2752, steps = 92  
shifted from previous position = 5.3  
rotated from previous position = 5.46 degrees  
atoms outside contour = 1850, contour level = 0.2532  
  
Position of PredictAndBuild_7_overall_best.pdb (#78) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.22705266 -0.96732791 -0.11279981 326.50448848  
-0.84045401 0.13610962 0.52451047 175.87350921  
-0.49202048 0.21389455 -0.84389867 316.29589561  
Axis -0.61344445 0.74893397 0.25056699  
Axis point 262.22373167 0.00000000 100.11436660  
Rotation angle (degrees) 165.33460884  
Shift along axis 10.67858762  
  

> fitmap #79 inMap #25

Fit molecule PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb
(#79) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6818
atoms  
average map value = 0.2107, steps = 172  
shifted from previous position = 11.4  
rotated from previous position = 5.55 degrees  
atoms outside contour = 4196, contour level = 0.2532  
  
Position of PredictAndBuild_7_superposed_predicted_untrimmed_cycle_1.pdb (#79)
relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.68234026 -0.66974665 -0.29300373 396.66689712  
-0.70556204 0.49846977 0.50369643 102.82972208  
-0.19129550 0.55042467 -0.81267381 199.71422066  
Axis 0.39762109 -0.86545829 -0.30476124  
Axis point 218.52168169 0.00000000 88.43752525  
Rotation angle (degrees) 176.63137373  
Shift along axis 7.86313588  
  

> fitmap #80 inMap #25

Fit molecule PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb
(#80) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6818
atoms  
average map value = 0.2002, steps = 128  
shifted from previous position = 3.93  
rotated from previous position = 13.2 degrees  
atoms outside contour = 4363, contour level = 0.2532  
  
Position of PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb (#80)
relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.61808214 -0.74524170 -0.25017850 390.14177001  
-0.76859940 0.50608871 0.39131723 125.96407520  
-0.16501341 0.43415324 -0.88559671 224.77237006  
Axis 0.43643009 -0.86769550 -0.23797752  
Axis point 223.54405179 0.00000000 100.58607108  
Rotation angle (degrees) 177.18705406  
Shift along axis 7.48037378  
  

> fitmap #81 inMap #25

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 239 atoms  
average map value = 0.2847, steps = 56  
shifted from previous position = 2.17  
rotated from previous position = 9.62 degrees  
atoms outside contour = 73, contour level = 0.2532  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#81) relative
to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.00169329 -0.79343761 -0.60864924 319.68781006  
-0.93882519 -0.20835191 0.27422025 280.49121917  
-0.34438989 0.57187957 -0.74454641 207.08413091  
Axis 0.70242609 -0.62360775 -0.34309032  
Axis point 0.00000000 266.91836814 201.99199878  
Rotation angle (degrees) 167.76748361  
Shift along axis -21.40799989  
  

> fitmap #82 inMap #25

Fit molecule copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#82) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4394 atoms  
average map value = 0.2705, steps = 120  
shifted from previous position = 6.58  
rotated from previous position = 13.2 degrees  
atoms outside contour = 2142, contour level = 0.2532  
  
Position of copy of
PredictAndBuild_7_overall_best_superposed_predicted_models.pdb (#82) relative
to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.08911154 -0.97740547 -0.19167078 312.61104116  
-0.86513544 -0.01940313 0.50116283 207.38914458  
-0.49355830 0.21048058 -0.84385907 317.01597391  
Axis -0.66998680 0.69581356 0.25876858  
Axis point 280.81289084 0.00000000 94.39286792  
Rotation angle (degrees) 167.47114130  
Shift along axis 16.89268056  
  

> fitmap #83 inMap #25

Fit molecule copy of PredictAndBuild_7_overall_best.pdb (#83) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3367 atoms  
average map value = 0.2736, steps = 104  
shifted from previous position = 4.19  
rotated from previous position = 7.76 degrees  
atoms outside contour = 1660, contour level = 0.2532  
  
Position of copy of PredictAndBuild_7_overall_best.pdb (#83) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.20610544 -0.97397844 -0.09426847 320.31886481  
-0.84612639 0.12899838 0.51713592 179.53786545  
-0.49151875 0.18634757 -0.85069613 321.39018439  
Axis -0.62117839 0.74598543 0.24008987  
Axis point 263.85010261 0.00000000 102.01189567  
Rotation angle (degrees) 164.55823923  
Shift along axis 12.12000484  
  

> hide #83 models

> hide #76 models

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best_superposed_predicted_models.pdb

Chain information for
PredictAndBuild_4_overall_best_superposed_predicted_models.pdb #84  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best.pdb

Chain information for PredictAndBuild_4_overall_best.pdb #85  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_superposed_predicted_untrimmed_cycle_1.pdb

Chain information for
PredictAndBuild_4_superposed_predicted_untrimmed_cycle_1.pdb #86  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_superposed_predicted_untrimmed_cycle_2.pdb

Chain information for
PredictAndBuild_4_superposed_predicted_untrimmed_cycle_2.pdb #87  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/PredictAndBuildCryoEM_4/PredictAndBuild_4_superposed_predicted_untrimmed_cycle_3.pdb

Chain information for
PredictAndBuild_4_superposed_predicted_untrimmed_cycle_3.pdb #88  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> ui tool show Matchmaker

> matchmaker #86-88#!84-85 to #83

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
PredictAndBuild_4_superposed_predicted_untrimmed_cycle_1.pdb, chain A (#86),
sequence alignment score = 2398.8  
RMSD between 245 pruned atom pairs is 0.859 angstroms; (across all 431 pairs:
6.247)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
PredictAndBuild_4_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#87),
sequence alignment score = 2398.8  
RMSD between 253 pruned atom pairs is 0.822 angstroms; (across all 431 pairs:
5.398)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
PredictAndBuild_4_superposed_predicted_untrimmed_cycle_3.pdb, chain A (#88),
sequence alignment score = 2398.8  
RMSD between 255 pruned atom pairs is 0.834 angstroms; (across all 431 pairs:
5.572)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
PredictAndBuild_4_overall_best_superposed_predicted_models.pdb, chain A (#84),
sequence alignment score = 2353  
RMSD between 261 pruned atom pairs is 0.933 angstroms; (across all 426 pairs:
5.270)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
PredictAndBuild_4_overall_best.pdb, chain A (#85), sequence alignment score =
2185.7  
RMSD between 274 pruned atom pairs is 0.698 angstroms; (across all 415 pairs:
4.042)  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_0.cif"

Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif #89  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_1.cif"

Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_1.cif #90  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_2.cif"

Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_2.cif #91  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_3.cif"

Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_3.cif #92  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_20250704_copi_abbprimedgz_trucadg/fold_20250704_copi_abbprimedgz_trucadg_model_4.cif"

Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_4.cif #93  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/COPI_soluble_job160_dhelix.pdb"

Chain information for COPI_soluble_job160_dhelix.pdb #94  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/COPI_soluble_job155_dhelix.pdb"

Chain information for COPI_soluble_job155_dhelix.pdb #95  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/COPI_soluble_job140_dhelix.pdb"

Chain information for COPI_soluble_job140_dhelix.pdb #96  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/COPI_soluble_job150_dhelix.pdb"

Chain information for COPI_soluble_job150_dhelix.pdb #97  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/COPI_soluble_job145_dhelix.pdb"

Chain information for COPI_soluble_job145_dhelix.pdb #98  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
  

> ui tool show Matchmaker

> matchmaker #89-93#!94-98 to #83

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
fold_20250704_copi_abbprimedgz_trucadg_model_0.cif, chain E (#89), sequence
alignment score = 2394.6  
RMSD between 254 pruned atom pairs is 1.108 angstroms; (across all 431 pairs:
2.715)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
fold_20250704_copi_abbprimedgz_trucadg_model_1.cif, chain E (#90), sequence
alignment score = 2394.6  
RMSD between 252 pruned atom pairs is 1.085 angstroms; (across all 431 pairs:
2.724)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
fold_20250704_copi_abbprimedgz_trucadg_model_2.cif, chain E (#91), sequence
alignment score = 2391  
RMSD between 245 pruned atom pairs is 1.089 angstroms; (across all 431 pairs:
2.930)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
fold_20250704_copi_abbprimedgz_trucadg_model_3.cif, chain E (#92), sequence
alignment score = 2401.8  
RMSD between 243 pruned atom pairs is 1.065 angstroms; (across all 431 pairs:
3.641)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
fold_20250704_copi_abbprimedgz_trucadg_model_4.cif, chain E (#93), sequence
alignment score = 2401.8  
RMSD between 241 pruned atom pairs is 1.095 angstroms; (across all 431 pairs:
2.725)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
COPI_soluble_job160_dhelix.pdb, chain M (#94), sequence alignment score =
1452.2  
RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
1.700)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
COPI_soluble_job155_dhelix.pdb, chain M (#95), sequence alignment score =
1452.2  
RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
1.700)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
COPI_soluble_job140_dhelix.pdb, chain M (#96), sequence alignment score =
1452.2  
RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
1.700)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
COPI_soluble_job150_dhelix.pdb, chain M (#97), sequence alignment score =
1452.2  
RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
1.700)  
  
Matchmaker copy of PredictAndBuild_7_overall_best.pdb, chain A (#83) with
COPI_soluble_job145_dhelix.pdb, chain M (#98), sequence alignment score =
1452.2  
RMSD between 239 pruned atom pairs is 1.088 angstroms; (across all 282 pairs:
1.700)  
  

> hide #86-93#!84-85,94-98 atoms

> show #86-93#!84-85,94-98 cartoons

> hide #93 models

> hide #92 models

> hide #91 models

> hide #90 models

> hide #89 models

> hide #88 models

> hide #87 models

> hide #86 models

> hide #!85 models

> hide #!84 models

> hide #!98 models

> hide #!97 models

> hide #!96 models

> hide #!95 models

> hide #!94 models

> show #89 models

> fitmap #89 inMap #25

Fit molecule fold_20250704_copi_abbprimedgz_trucadg_model_0.cif (#89) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 31307 atoms  
average map value = 0.1729, steps = 144  
shifted from previous position = 3.16  
rotated from previous position = 14.3 degrees  
atoms outside contour = 21652, contour level = 0.2532  
  
Position of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif (#89) relative
to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.05328171 -0.76106194 -0.64648727 140.92255080  
0.28101753 0.63267016 -0.72163538 147.85576557  
0.95822242 -0.14322428 0.24758149 143.21536141  
Axis 0.28936539 -0.80279829 0.52132770  
Axis point 9.80405567 0.00000000 205.08316869  
Rotation angle (degrees) 91.90447951  
Shift along axis -3.25811224  
  

> hide #89 models

> show #!94 models

> fitmap #94 inMap #25

Fit molecule COPI_soluble_job160_dhelix.pdb (#94) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms  
average map value = 0.2718, steps = 204  
shifted from previous position = 15.7  
rotated from previous position = 16.6 degrees  
atoms outside contour = 14003, contour level = 0.2532  
  
Position of COPI_soluble_job160_dhelix.pdb (#94) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.94072620 0.21431989 -0.26287109 429.26780955  
0.04392373 -0.69153884 -0.72100259 611.48757588  
-0.33631076 -0.68981230 0.64113497 251.13731297  
Axis 0.16577200 0.39032157 -0.90563167  
Axis point 252.69703805 349.04589066 0.00000000  
Rotation angle (degrees) 174.60186768  
Shift along axis 82.39947160  
  

> fitmap #95 inMap #25

Fit molecule COPI_soluble_job155_dhelix.pdb (#95) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms  
average map value = 0.2423, steps = 164  
shifted from previous position = 15.2  
rotated from previous position = 11.8 degrees  
atoms outside contour = 15830, contour level = 0.2532  
  
Position of COPI_soluble_job155_dhelix.pdb (#95) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.93495608 0.23558445 -0.26524914 421.51639111  
0.02686846 -0.69850918 -0.71509651 616.29442709  
-0.35374457 -0.67571066 0.64674561 248.96083246  
Axis 0.17116994 0.38459904 -0.90707466  
Axis point 252.83551002 347.97043032 0.00000000  
Rotation angle (degrees) 173.39355126  
Shift along axis 83.35111726  
  

> fitmap #96 inMap #25

Fit molecule COPI_soluble_job140_dhelix.pdb (#96) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms  
average map value = 0.2622, steps = 256  
shifted from previous position = 18.3  
rotated from previous position = 12.3 degrees  
atoms outside contour = 14721, contour level = 0.2532  
  
Position of COPI_soluble_job140_dhelix.pdb (#96) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.93956714 0.21928330 -0.26292285 427.34338098  
0.03882046 -0.69477206 -0.71818156 612.97301969  
-0.34015668 -0.68498658 0.64427232 249.37443237  
Axis 0.16673989 0.38794901 -0.90647304  
Axis point 252.59063007 348.46957852 0.00000000  
Rotation angle (degrees) 174.28724830  
Shift along axis 83.00626481  
  

> fitmap #97 inMap #25

Fit molecule COPI_soluble_job150_dhelix.pdb (#97) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms  
average map value = 0.2628, steps = 212  
shifted from previous position = 21  
rotated from previous position = 15.7 degrees  
atoms outside contour = 14726, contour level = 0.2532  
  
Position of COPI_soluble_job150_dhelix.pdb (#97) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.94025104 0.21735184 -0.26208044 427.88998347  
0.04057084 -0.69272872 -0.72005619 612.48408539  
-0.33805619 -0.68766641 0.64252076 250.33040167  
Axis 0.16599686 0.38937389 -0.90599836  
Axis point 252.53671335 348.85846385 0.00000000  
Rotation angle (degrees) 174.40123581  
Shift along axis 82.71476836  
  

> fitmap #98 inMap #25

Fit molecule COPI_soluble_job145_dhelix.pdb (#98) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 27657 atoms  
average map value = 0.2587, steps = 272  
shifted from previous position = 18  
rotated from previous position = 11.9 degrees  
atoms outside contour = 15067, contour level = 0.2532  
  
Position of COPI_soluble_job145_dhelix.pdb (#98) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.93993457 0.21619613 -0.26416328 429.04174114  
0.04215368 -0.69443036 -0.71832412 612.05358105  
-0.33874190 -0.68631312 0.64360564 249.64587097  
Axis 0.16669352 0.38835946 -0.90630580  
Axis point 252.87215354 348.49166546 0.00000000  
Rotation angle (degrees) 174.49011360  
Shift along axis 82.95977526  
  

> hide #!94 models

> show #!94 models

> hide #!94 models

> show #!95 models

> hide #!95 models

> show #!94 models

> hide #!50 models

> show #!33 models

> hide #!25 models

> hide #!33 models

> show #!25 models

> close #1

> close #4

> close #6

> close #8

> close #10

> close #12

> close #14

> close #16

> close #18

> close #20

> close #22

> close #24

> close #26

> close #28

> close #41

> hide #!25 models

> hide #!94 models

> show #!96 models

> show #!95 models

> hide #!95 models

> show #!94 models

> hide #!94 models

> show #!97 models

> hide #!97 models

> show #!98 models

> hide #!98 models

> hide #!96 models

> show #!94 models

> split #94 chains

Split COPI_soluble_job160_dhelix.pdb (#94) into 14 models  
Chain information for COPI_soluble_job160_dhelix.pdb D #94.1  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb E #94.2  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb F #94.3  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb G #94.4  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb H #94.5  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb I #94.6  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb J #94.7  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb K #94.8  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb L #94.9  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb M #94.10  
---  
Chain | Description  
M | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb N #94.11  
---  
Chain | Description  
N | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb O #94.12  
---  
Chain | Description  
O | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb P #94.13  
---  
Chain | Description  
P | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb Q #94.14  
---  
Chain | Description  
Q | No description available  
  

> show #!95 models

> hide #!95 models

> close #95

> close #96

> close #97

> close #98

> hide #94.1 models

> hide #94.2 models

> hide #94.3 models

> hide #94.4 models

> hide #94.5 models

> hide #!94.6 models

> hide #!94.7 models

> hide #94.8 models

> show #94.8 models

> hide #94.8 models

> hide #94.12 models

> hide #!94.13 models

> hide #!94.14 models

> show #89 models

> show #!25 models

> hide #89 models

> show #90 models

> show #89 models

> hide #89 models

> hide #90 models

> show #91 models

> hide #91 models

> show #92 models

> hide #92 models

> show #93 models

> hide #93 models

> show #88 models

> hide #88 models

> show #78 models

> hide #78 models

> show #!81 models

> hide #!81 models

> show #!81 models

> hide #!81 models

> show #!82 models

> hide #!82 models

> show #79 models

> hide #79 models

> show #80 models

> fitmap #80 inMap #25

Fit molecule PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb
(#80) to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6818
atoms  
average map value = 0.2002, steps = 28  
shifted from previous position = 0.0204  
rotated from previous position = 0.023 degrees  
atoms outside contour = 4363, contour level = 0.2532  
  
Position of PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb (#80)
relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.61827994 -0.74501686 -0.25035934 390.17808029  
-0.76844646 0.50614879 0.39153982 125.89539509  
-0.16498469 0.43446897 -0.88544721 224.70859005  
Axis 0.43631396 -0.86771240 -0.23812878  
Axis point 223.52898003 0.00000000 100.56670382  
Rotation angle (degrees) 177.18018194  
Shift along axis 7.48956636  
  

> ui tool show Matchmaker

> matchmaker #80 to #94.9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_soluble_job160_dhelix.pdb L, chain L (#94.9) with
PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#80),
sequence alignment score = 751  
RMSD between 111 pruned atom pairs is 0.761 angstroms; (across all 149 pairs:
2.111)  
  

> ui tool show Matchmaker

> matchmaker #80 to #94.10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_soluble_job160_dhelix.pdb M, chain M (#94.10) with
PredictAndBuild_7_superposed_predicted_untrimmed_cycle_2.pdb, chain A (#80),
sequence alignment score = 1461.2  
RMSD between 282 pruned atom pairs is 0.718 angstroms; (across all 283 pairs:
0.728)  
  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250706_W20_COPI_cyto_alignments.cxs"

> show #89 models

> split #89 chains

Split fold_20250704_copi_abbprimedgz_trucadg_model_0.cif (#89) into 6 models  
Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif A
#89.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif B
#89.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif C
#89.3  
---  
Chain | Description  
C | No description available  
  
Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif D
#89.4  
---  
Chain | Description  
D | No description available  
  
Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E
#89.5  
---  
Chain | Description  
E | No description available  
  
Chain information for fold_20250704_copi_abbprimedgz_trucadg_model_0.cif F
#89.6  
---  
Chain | Description  
F | No description available  
  

> show #90 models

> hide #90 models

> close #90

> close #91-93

> hide #89.1 models

> hide #89.2 models

> show #89.2 models

> hide #89.3 models

> hide #89.4 models

> hide #89.6 models

> hide #80 models

> hide #89.2 models

> hide #!94 models

> show #!94 models

> hide #!94 models

> show #!94 models

> hide #!94 models

> show #!94 models

> hide #!94 models

> combine #89.5

[Repeated 1 time(s)]

> hide #!89 models

> hide #!25 models

> hide #4 models

Drag select of 2 residues  

> select up

41 atoms, 40 bonds, 5 residues, 1 model selected  

> delete sel

Drag select of 23 residues  

> select up

293 atoms, 299 bonds, 37 residues, 1 model selected  

> delete sel

Drag select of 11 residues, 1 pseudobonds  

> delete sel

> show #!94 models

> hide #!94 models

> show #!94 models

Drag select of 14 residues  

> select up

308 atoms, 312 bonds, 41 residues, 1 model selected  

> delete sel

> hide #!94 models

> show #!94 models

> hide #!94 models

Drag select of 113 residues  

> select up

1028 atoms, 1043 bonds, 131 residues, 1 model selected  

> delete sel

> fitmap #1 inMap #25

Fit molecule copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#1)
to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 3497 atoms  
average map value = 0.3397, steps = 120  
shifted from previous position = 9.43  
rotated from previous position = 15.4 degrees  
atoms outside contour = 1097, contour level = 0.2532  
  
Position of copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#1)
relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.28192072 -0.63906244 -0.71562553 141.48853049  
0.25178912 0.76901734 -0.58754964 138.75926341  
0.92580935 -0.01454430 0.37771089 139.40543708  
Axis 0.29331865 -0.84024256 0.45602259  
Axis point -12.05331597 0.00000000 214.52876942  
Rotation angle (degrees) 77.62410125  
Shift along axis -11.51818437  
  

> show #!25 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #4 models

> hide #!25 models

> hide #4 models

> show #!1 models

> show #4 models

> show #!25 models

> hide #!1 models

> hide #!25 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #4 models

> show #!1 models

> hide #!1 models

> show #4 models

Drag select of 17 residues  

> select up

334 atoms, 340 bonds, 42 residues, 1 model selected  

> delete sel

Drag select of 9 residues  

> select up

183 atoms, 186 bonds, 22 residues, 1 model selected  

> delete sel

Drag select of 19 residues  

> select up

215 atoms, 218 bonds, 30 residues, 1 model selected  

> select clear

Drag select of 9 residues  

> delete sel

Drag select of 7 residues  

> select clear

Drag select of 13 residues  

> select clear

Drag select of 15 residues  

> delete sel

> show #!25 models

> fitmap #4 inMap #25

Fit molecule copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#4)
to map W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4566 atoms  
average map value = 0.3172, steps = 112  
shifted from previous position = 8.14  
rotated from previous position = 15.5 degrees  
atoms outside contour = 1647, contour level = 0.2532  
  
Position of copy of fold_20250704_copi_abbprimedgz_trucadg_model_0.cif E (#4)
relative to W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.28339787 -0.63805488 -0.71594107 141.54232791  
0.25944422 0.76971940 -0.58328444 139.21027357  
0.92324122 -0.02044520 0.38367649 139.06277017  
Axis 0.28838113 -0.83986547 0.45985032  
Axis point -12.84705545 0.00000000 215.45471328  
Rotation angle (degrees) 77.38510832  
Shift along axis -12.15170567  
  

> select #4/E:584

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete sel

> select #4/E:583

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete sel

> hide #!4 models

> show #!4 models

> combine #4

> hide #!4 models

> rename #4 gamma-COPI_v1

> combine #64 #66 #67 #70 #71 #4

Remapping chain ID 'B' in beta-COPI #66 to 'D'  
Remapping chain ID 'C' in beta-COPI #66 to 'E'  
Remapping chain ID 'A' in betaprime-COPI #67 to 'F'  
Remapping chain ID 'B' in betaprime-COPI #67 to 'G'  
Remapping chain ID 'C' in betaprime-COPI #67 to 'H'  
Remapping chain ID 'D' in betaprime-COPI #67 to 'I'  
Remapping chain ID 'A' in delta-COPI #70 to 'J'  
Remapping chain ID 'B' in delta-COPI #70 to 'K'  
Remapping chain ID 'A' in zeta-COPI #71 to 'L'  
Remapping chain ID 'E' in gamma-COPI_v1 #4 to 'M'  

> hide #!6 models

> fitmap #4 inMap #25

Fit molecule gamma-COPI_v1 (#4) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4552 atoms  
average map value = 0.3176, steps = 40  
shifted from previous position = 0.0254  
rotated from previous position = 0.0198 degrees  
atoms outside contour = 1637, contour level = 0.2532  
  
Position of gamma-COPI_v1 (#4) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.28348444 -0.63781373 -0.71612165 141.56919510  
0.25922020 0.76992233 -0.58311620 139.19563791  
0.92327756 -0.02032883 0.38359520 139.07316286  
Axis 0.28836144 -0.83999668 0.45962296  
Axis point -12.85164212 0.00000000 215.45181715  
Rotation angle (degrees) 77.37899637  
Shift along axis -12.17955787  
  

> fitmap #4 inMap #25

Fit molecule gamma-COPI_v1 (#4) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 4552 atoms  
average map value = 0.3176, steps = 40  
shifted from previous position = 0.0216  
rotated from previous position = 0.0256 degrees  
atoms outside contour = 1634, contour level = 0.2532  
  
Position of gamma-COPI_v1 (#4) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
0.28351557 -0.63806429 -0.71588608 141.55271505  
0.25957296 0.76971101 -0.58323823 139.22244867  
0.92316889 -0.02046756 0.38384929 139.05660502  
Axis 0.28835533 -0.83982741 0.45993599  
Axis point -12.85662194 0.00000000 215.49138830  
Rotation angle (degrees) 77.37682658  
Shift along axis -12.14821127  
  

> fitmap #64 inMap #25

Fit molecule alpha-COPI (#64) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6628 atoms  
average map value = 0.3537, steps = 72  
shifted from previous position = 0.413  
rotated from previous position = 1.38 degrees  
atoms outside contour = 1857, contour level = 0.2532  
  
Position of alpha-COPI (#64) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.36586447 -0.91732918 -0.15700440 275.35878138  
-0.79670780 0.22151549 0.56230559 163.87536925  
-0.48104042 0.33081427 -0.81188796 242.97769193  
Axis -0.55633921 0.77875030 0.28988732  
Axis point 211.74531088 0.00000000 70.70797620  
Rotation angle (degrees) 167.99197292  
Shift along axis 44.86125869  
  

> fitmap #66 inMap #25

Fit molecule beta-COPI (#66) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 6621 atoms  
average map value = 0.2922, steps = 64  
shifted from previous position = 0.113  
rotated from previous position = 1.01 degrees  
atoms outside contour = 2335, contour level = 0.2532  
  
Position of beta-COPI (#66) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.33217082 -0.91999498 -0.20801872 277.50726921  
-0.77605969 0.14122581 0.61464349 158.87975673  
-0.53609132 0.36560157 -0.76088211 242.10904879  
Axis -0.57078454 0.75191666 0.32988838  
Axis point 215.84062714 0.00000000 64.11235965  
Rotation angle (degrees) 167.39915972  
Shift along axis 40.93643893  
  

> fitmap #70 inMap #25

Fit molecule delta-COPI (#70) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1431 atoms  
average map value = 0.2517, steps = 140  
shifted from previous position = 0.914  
rotated from previous position = 5.42 degrees  
atoms outside contour = 770, contour level = 0.2532  
  
Position of delta-COPI (#70) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.34798043 -0.93749415 -0.00378617 175.64116001  
0.05522224 -0.01646557 -0.99833831 178.10409974  
0.93587399 -0.34761128 0.05750022 154.89993905  
Axis 0.42983493 -0.62068846 0.65573452  
Axis point -39.53177108 213.69242364 0.00000000  
Rotation angle (degrees) 130.80395777  
Shift along axis 66.52278419  
  

> fitmap #71 inMap #25

Fit molecule zeta-COPI (#71) to map
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) using 1420 atoms  
average map value = 0.2522, steps = 180  
shifted from previous position = 10.5  
rotated from previous position = 19.5 degrees  
atoms outside contour = 661, contour level = 0.2532  
  
Position of zeta-COPI (#71) relative to
W20_J4027_005_volume_map_gammazeta_local.mrc (#25) coordinates:  
Matrix rotation and translation  
-0.32469740 0.40326773 0.85553887 117.00818860  
0.20978479 -0.85131177 0.48089357 145.18762928  
0.92225916 0.33562393 0.19181929 99.65953140  
Axis -0.57881168 -0.26584003 -0.77091253  
Axis point 25.03383553 54.96126454 0.00000000  
Rotation angle (degrees) 172.79097233  
Shift along axis -183.15117020  
  

> show #71 models

> hide #71 models

> show #71 models

> hide #71 models

> close #8

> combine #64 #66 #67 #70 #71 #4

Remapping chain ID 'B' in beta-COPI #66 to 'D'  
Remapping chain ID 'C' in beta-COPI #66 to 'E'  
Remapping chain ID 'A' in betaprime-COPI #67 to 'F'  
Remapping chain ID 'B' in betaprime-COPI #67 to 'G'  
Remapping chain ID 'C' in betaprime-COPI #67 to 'H'  
Remapping chain ID 'D' in betaprime-COPI #67 to 'I'  
Remapping chain ID 'A' in delta-COPI #70 to 'J'  
Remapping chain ID 'B' in delta-COPI #70 to 'K'  
Remapping chain ID 'A' in zeta-COPI #71 to 'L'  
Remapping chain ID 'E' in gamma-COPI_v1 #4 to 'M'  

> rename #8 COPI_cyto_for_J4027_v1

> cd "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI"

Current working directory is: /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/Processing/W20_MM_cyto_COPI  

> save COPI_cyto_for_J4027_v1.pdb #8

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/cc_map.ccp4

Opened cc_map.ccp4 as #10, grid size 240,240,240, pixel 1.19, shown at level
0.697, step 1, values float32  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/composite_map.ccp4

Opened composite_map.ccp4 as #12, grid size 240,240,240, pixel 1.19, shown at
level 5.35, step 1, values float32  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/composite_map.pdb

Summary of feedback from opening
/Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/composite_map.pdb  
---  
warning | Ignored bad PDB record found on line 27366  
  
Chain information for composite_map.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/contribution_map_1.ccp4

Opened contribution_map_1.ccp4 as #16, grid size 240,240,240, pixel 1.19,
shown at level 1, step 1, values float32  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_8/contribution_map_2.ccp4

Opened contribution_map_2.ccp4 as #18, grid size 240,240,240, pixel 1.19,
shown at level 0.47, step 1, values float32  

> hide #!8 models

> hide #!10 models

> hide #!12 models

> hide #!14 models

> hide #!16 models

> hide #!18 models

> hide #!25 models

> show #!10 models

> show #!12 models

> show #!14 models

> show #!16 models

> show #!18 models

> close #18

> hide #!14 models

> close #10

> close #12

> show #!14 models

> hide #!14 models

> hide #!16 models

> show #!16 models

> close #16

> close #14

> show #!4 models

> show #!25 models

> hide #!25 models

> show #!23 models

> show #!27 models

> show #!25 models

> hide #!27 models

> show #!32 models

> hide #!32 models

> show #!33 models

> hide #!25 models

> hide #!23 models

> hide #!33 models

> show #!2 models

> hide #!2 models

> show #!3 models

> close #3

> show #!5 models

> close #5

> show #!7 models

> hide #!7 models

> show #!9 models

> show #!23 models

> show #!25 models

> show #!27 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!23 models

> hide #!27 models

> hide #!25 models

> show #!7 models

> hide #!7 models

> show #!9 models

> hide #!9 models

> show #!11 models

> close #11

> show #!13 models

> show #!15 models

> hide #!15 models

> show #!17 models

> hide #!17 models

> show #!19 models

> show #!17 models

> show #!15 models

> show #!21 models

> hide #!21 models

> hide #!19 models

> hide #!17 models

> hide #!15 models

> hide #!13 models

> show #!29 models

> hide #!29 models

> show #!30 models

> show #!29 models

> show #!31 models

> hide #!31 models

> hide #!30 models

> hide #!29 models

> show #!32 models

> hide #!4 models

> hide #!32 models

> show #!13 models

> show #!15 models

> hide #!15 models

> show #!17 models

> hide #!17 models

> show #!19 models

> show #!21 models

> hide #!21 models

> hide #!19 models

> hide #!13 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!4 models

> show #!7 models

> hide #!7 models

> close #1

> hide #!4 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_A.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_B.mrc"

Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #1.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #1.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #1.1 level 0.2608

> volume #1.2 level 0.2582

> hide #!1 models

> close #1

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/J3623_auto_sharpened_map.ccp4"

Opened J3623_auto_sharpened_map.ccp4 as #1, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  

> hide #!2 models

> volume #1 level 2.641

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_22/denmod_resolution_map.ccp4

Opened denmod_resolution_map.ccp4 as #3, grid size 104,126,128, pixel 1.19,
shown at level 11.3, step 1, values float32  

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> hide #!3 models

> close #3

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_22/J3623_denmod_map.ccp4

Opened J3623_denmod_map.ccp4 as #3, grid size 104,126,128, pixel 1.19, shown
at level 0.531, step 1, values float32  

> volume #3 level 0.2174

> show #!66 models

> show #!64 models

> hide #!64 models

> show #!64 models

> hide #!66 models

> hide #!64 models

> show #!70 models

> volume #3 level 0.1325

> volume #3 level 0.25

> show #!66 models

> color #5 gammav3

> color #4 gammav3

> hide #!3 models

> close #3

> close #2

> close #1

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure.mrc"

Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/J3623_auto_sharpened_map.ccp4"

Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32  

> hide #!70 models

> hide #!66 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_A.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3623_008_volume_map_half_B.mrc"

Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  

> rename #3 J3623_half_maps

> combine #4

> close #4

> combine #5

[Repeated 1 time(s)]

> close #4

> close #5

> show #!6 models

> hide #!6 models

> close #6

> show #!7 models

> hide #!7 models

> close #7

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc"

Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32  

> select add #4

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.25307,-0.96623,-0.048581,315.98,-0.86086,0.202,0.46702,167.97,-0.44144,0.16001,-0.88291,294.43

> view matrix models
> #4,-0.14459,-0.98817,-0.051169,305.09,-0.67606,0.060895,0.73433,127.29,-0.72252,0.14077,-0.67686,306.41

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.14459,-0.98817,-0.051169,320.79,-0.67606,0.060895,0.73433,129.24,-0.72252,0.14077,-0.67686,326.78

> fitmap #4 inMap #1

Fit map
W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc in map
W20_J3623_consensus_structure.mrc using 138206 points  
correlation = 0.982, correlation about mean = 0.7994, overlap = 2.043e+04  
steps = 156, shift = 6.09, angle = 17.9 degrees  
  
Position of
W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc (#4)
relative to W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33998516 -0.91904572 -0.19941175 353.84995809  
-0.77678119 0.15490951 0.61042118 146.12290386  
-0.53011420 0.36243344 -0.76656437 277.61520820  
Axis -0.56728131 0.75649433 0.32543548  
Axis point 252.00716027 0.00000000 81.49850043  
Rotation angle (degrees) 167.37461303  
Shift along axis 0.15451903  
  

> volume resample #4 onGrid #1

Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
resampled as #5, grid size 240,240,240, pixel 1.19, shown at step 1, values
float32  

> select subtract #4

Nothing selected  

> close #4

> cd "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI"

Current working directory is: /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/Processing/W20_MM_cyto_COPI  

> save W20_J3987_consensus_resampled.mrc #5

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_consensus_resampled.mrc"

Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32  

> hide #!5 models

> fitmap #4 inMap #1

Fit map W20_J3987_consensus_resampled.mrc in map
W20_J3623_consensus_structure.mrc using 138117 points  
correlation = 0.9803, correlation about mean = 0.7915, overlap = 2.075e+04  
steps = 28, shift = 0.021, angle = 0.00696 degrees  
  
Position of W20_J3987_consensus_resampled.mrc (#4) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00006999 -0.00003626 -0.00018519  
-0.00006999 0.99999999 -0.00009239 0.04429622  
0.00003626 0.00009240 1.00000000 -0.01684920  
Axis 0.76076686 -0.29856000 -0.57627746  
Axis point 0.00000000 205.18615312 467.59873778  
Rotation angle (degrees) 0.00695857  
Shift along axis -0.00365615  
  

> close #5

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3987_004_volume_map_half_B.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3987_004_volume_map_half_A.mrc"

Opened cryosparc_P126_J3987_004_volume_map_half_B.mrc as #5.1, grid size
240,240,240, pixel 1.2, shown at level 0.274, step 1, values float32  
Opened cryosparc_P126_J3987_004_volume_map_half_A.mrc as #5.2, grid size
240,240,240, pixel 1.2, shown at level 0.274, step 1, values float32  

> select add #5.1

2 models selected  

> select add #5.2

4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #5.1,-0.38208,-0.71776,-0.5821,371.56,-0.90525,0.41738,0.079546,196.1,0.18586,0.55733,-0.80922,143.66,#5.2,-0.38208,-0.71776,-0.5821,371.56,-0.90525,0.41738,0.079546,196.1,0.18586,0.55733,-0.80922,143.66

> view matrix models
> #5.1,-0.42487,-0.88152,-0.20596,349.25,-0.72637,0.19619,0.6587,124.33,-0.54025,0.42946,-0.72366,248.21,#5.2,-0.42487,-0.88152,-0.20596,349.25,-0.72637,0.19619,0.6587,124.33,-0.54025,0.42946,-0.72366,248.21

> ui mousemode right "translate selected models"

> view matrix models
> #5.1,-0.42487,-0.88152,-0.20596,359.35,-0.72637,0.19619,0.6587,126.62,-0.54025,0.42946,-0.72366,262.21,#5.2,-0.42487,-0.88152,-0.20596,359.35,-0.72637,0.19619,0.6587,126.62,-0.54025,0.42946,-0.72366,262.21

> fitmap #5.1 inMap #1

Fit map cryosparc_P126_J3987_004_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138219 points  
correlation = 0.9769, correlation about mean = 0.7541, overlap = 2.056e+04  
steps = 80, shift = 1.82, angle = 5.92 degrees  
  
Position of cryosparc_P126_J3987_004_volume_map_half_B.mrc (#5.1) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34088191 -0.91883476 -0.19885219 353.85897435  
-0.77626012 0.15578649 0.61086069 145.85323816  
-0.53030155 0.36259239 -0.76635958 277.59067344  
Axis -0.56685311 0.75677442 0.32553039  
Axis point 251.87895379 0.00000000 81.50551240  
Rotation angle (degrees) 167.35038692  
Shift along axis 0.15614218  
  

> fitmap #5.2 inMap #1

Fit map cryosparc_P126_J3987_004_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138231 points  
correlation = 0.9769, correlation about mean = 0.7539, overlap = 2.061e+04  
steps = 80, shift = 1.81, angle = 6.04 degrees  
  
Position of cryosparc_P126_J3987_004_volume_map_half_A.mrc (#5.2) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33893365 -0.91937774 -0.19967107 353.79911788  
-0.77742964 0.15417077 0.60978235 146.41544867  
-0.52983688 0.36190597 -0.76700517 277.70182392  
Axis -0.56776952 0.75625634 0.32513709  
Axis point 252.14174450 0.00000000 81.52863602  
Rotation angle (degrees) 167.39140634  
Shift along axis 0.14242009  
  

> select subtract #5.2

2 models selected  

> select subtract #5.1

Nothing selected  

> volume resample #5.1 #5.2 onGrid #1

Opened cryosparc_P126_J3987_004_volume_map_half_B.mrc resampled as #6, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J3987_004_volume_map_half_A.mrc resampled as #7, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J3987_halfA_consensus_resampled.mrc #7

> save W20_J3987_halfB_consensus_resampled.mrc #6

> close #5-7#5.1-2

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_halfB_consensus_resampled.mrc"

Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32  

> rename #5 J3987_half_maps

> show #!8 models

> hide #!8 models

> combine #8

[Repeated 2 time(s)]

> close #6-8

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_005_volume_map_bprime_local.mrc"

Opened W20_J4021_005_volume_map_bprime_local.mrc as #6, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4021_005_volume_map_half_B.mrc"

Opened cryosparc_P126_J4021_005_volume_map_half_B.mrc as #7, grid size
240,240,240, pixel 1.19, shown at level 0.263, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4021_005_volume_map_half_A.mrc"

Opened cryosparc_P126_J4021_005_volume_map_half_A.mrc as #8, grid size
240,240,240, pixel 1.19, shown at level 0.262, step 1, values float32  

> volume resample #6 #7 #8 onGrid #1

Opened W20_J4021_005_volume_map_bprime_local.mrc resampled as #12, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4021_005_volume_map_half_B.mrc resampled as #14, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4021_005_volume_map_half_A.mrc resampled as #16, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> close #16

> close #14

> close #12

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> fitmap #6 #7 #8 inMap #1

Multiple maps for #6#7#8  

> show #!6 models

> show #!7 models

> show #!8 models

> fitmap #6 inMap #1

Fit map W20_J4021_005_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure.mrc using 138166 points  
correlation = 0.9132, correlation about mean = 0.2137, overlap = 1.684e+04  
steps = 52, shift = 0.553, angle = 0.278 degrees  
  
Position of W20_J4021_005_volume_map_bprime_local.mrc (#6) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999230 0.00368913 -0.00133441 -0.32621193  
-0.00369294 0.99998910 -0.00285852 0.49731748  
0.00132385 0.00286342 0.99999502 -0.37762592  
Axis 0.58922795 -0.27373864 -0.76018260  
Axis point 131.36464990 82.10529237 0.00000000  
Rotation angle (degrees) 0.27819836  
Shift along axis -0.04128355  
  

> fitmap #7 inMap #1

Fit map cryosparc_P126_J4021_005_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138066 points  
correlation = 0.907, correlation about mean = 0.2359, overlap = 1.707e+04  
steps = 68, shift = 0.546, angle = 0.314 degrees  
  
Position of cryosparc_P126_J4021_005_volume_map_half_B.mrc (#7) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999065 0.00386110 -0.00194507 -0.25775142  
-0.00386765 0.99998683 -0.00337455 0.61622992  
0.00193201 0.00338205 0.99999241 -0.53165616  
Axis 0.61572178 -0.35331456 -0.70431208  
Axis point 158.92151900 66.82584882 0.00000000  
Rotation angle (degrees) 0.31436809  
Shift along axis -0.00197431  
  

> fitmap #8 inMap #1

Fit map cryosparc_P126_J4021_005_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138185 points  
correlation = 0.9063, correlation about mean = 0.2362, overlap = 1.703e+04  
steps = 44, shift = 0.534, angle = 0.288 degrees  
  
Position of cryosparc_P126_J4021_005_volume_map_half_A.mrc (#8) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999293 0.00344362 -0.00151137 -0.26561114  
-0.00344864 0.99998850 -0.00333361 0.55833592  
0.00149988 0.00333880 0.99999330 -0.46926499  
Axis 0.66362765 -0.29949438 -0.68549359  
Axis point 159.76195443 73.25690596 0.00000000  
Rotation angle (degrees) 0.28804014  
Shift along axis -0.02180722  
  

> volume resample #6 #7 #8 onGrid #1

Opened W20_J4021_005_volume_map_bprime_local.mrc resampled as #12, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4021_005_volume_map_half_B.mrc resampled as #14, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4021_005_volume_map_half_A.mrc resampled as #16, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> hide #!10 models

> hide #!11 models

> close #13

> save W20_J4021_halfA_consensus_resampled.mrc #16

> save W20_J4021_halfB_consensus_resampled.mrc #14

> save W20_J4021_consensus_resampled.mrc #12

> close #6-8

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_consensus_resampled.mrc"

Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4021_halfB_consensus_resampled.mrc"

Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32  

> rename #7 J4021_half_maps

> combine #10

[Repeated 1 time(s)]

> combine #11

> close #8

> close #9

> hide #!18 models

> hide #!16 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!7 models

> hide #!6 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_bprime_local.mrc"

Opened W20_J4022_005_volume_map_bprime_local.mrc as #8, grid size 240,240,240,
pixel 1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_A.mrc"

Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc as #9, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"

Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"

Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  

> close #22

> close #20

> close #10

> close #11

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"

Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #10, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  

> fitmap #8 inMap #1

Fit map W20_J4022_005_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure.mrc using 138200 points  
correlation = 0.9195, correlation about mean = 0.2263, overlap = 1.667e+04  
steps = 64, shift = 0.329, angle = 0.376 degrees  
  
Position of W20_J4022_005_volume_map_bprime_local.mrc (#8) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997966 0.00237299 0.00592048 -1.40324868  
-0.00238223 0.99999595 0.00155423 -0.17561136  
-0.00591677 -0.00156830 0.99998127 1.18884605  
Axis -0.23775685 0.90131776 -0.36207456  
Axis point 184.53246236 0.00000000 247.89429522  
Rotation angle (degrees) 0.37624341  
Shift along axis -0.25510056  
  

> fitmap #9 inMap #1

Fit map cryosparc_P126_J4022_005_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138165 points  
correlation = 0.9121, correlation about mean = 0.2433, overlap = 1.687e+04  
steps = 52, shift = 0.339, angle = 0.357 degrees  
  
Position of cryosparc_P126_J4022_005_volume_map_half_A.mrc (#9) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998304 0.00160770 0.00559706 -1.23594018  
-0.00161999 0.99999628 0.00219278 -0.39387001  
-0.00559351 -0.00220181 0.99998193 1.22871953  
Axis -0.35302911 0.89896616 -0.25928803  
Axis point 207.94947596 0.00000000 236.35689026  
Rotation angle (degrees) 0.35661877  
Shift along axis -0.23634521  
  

> fitmap #10 inMap #1

Fit map cryosparc_P126_J4022_005_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138076 points  
correlation = 0.9128, correlation about mean = 0.2508, overlap = 1.688e+04  
steps = 64, shift = 0.335, angle = 0.335 degrees  
  
Position of cryosparc_P126_J4022_005_volume_map_half_B.mrc (#10) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998354 0.00229208 0.00525924 -1.29178101  
-0.00229810 0.99999671 0.00113989 -0.13676617  
-0.00525661 -0.00115196 0.99998552 0.99455043  
Axis -0.19587427 0.89873969 -0.39230121  
Axis point 169.08755660 -0.00000000 255.83594172  
Rotation angle (degrees) 0.33520093  
Shift along axis -0.26005386  
  

> volume resample #8 #9 #10 onGrid #1

Opened W20_J4022_005_volume_map_bprime_local.mrc resampled as #11, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc resampled as #20, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc resampled as #22, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4022_halfB_consensus_resampled.mrc #22

> save W20_J4022_half1_consensus_resampled.mrc #20

> save W20_J4022_halfA_consensus_resampled.mrc #20

> save W20_J4022_consensus_resampled.mrc #11

> close #8-10

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_consensus_resampled.mrc"

Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfB_consensus_resampled.mrc"

Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  

> rename #9 J4022_half_maps

> combine #13

[Repeated 1 time(s)]

> combine #18

> hide #!10 models

> close #10-17

> hide #!9 models

> hide #!8 models

> show #!25 models

> hide #!24 models

> hide #!26 models

> hide #!25 models

> hide #!22 models

> hide #!20 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_bprime_local.mrc"

Opened W20_J4023_003_volume_map_bprime_local.mrc as #10, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_A.mrc"

Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc as #11, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_B.mrc"

Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc as #12, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> fitmap #10 inMap #1

Fit map W20_J4023_003_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure.mrc using 138098 points  
correlation = 0.9217, correlation about mean = 0.2228, overlap = 1.65e+04  
steps = 52, shift = 0.377, angle = 0.32 degrees  
  
Position of W20_J4023_003_volume_map_bprime_local.mrc (#10) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998445 0.00551741 0.00081396 -1.06075152  
-0.00551761 0.99998475 0.00023719 0.41218042  
-0.00081264 -0.00024168 0.99999964 0.27797318  
Axis -0.04289152 0.14569399 -0.98839950  
Axis point 78.63485140 193.79218176 0.00000000  
Rotation angle (degrees) 0.31984208  
Shift along axis -0.16919909  
  

> fitmap #11 inMap #1

Fit map cryosparc_P126_J4023_003_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138113 points  
correlation = 0.9179, correlation about mean = 0.2457, overlap = 1.663e+04  
steps = 52, shift = 0.377, angle = 0.301 degrees  
  
Position of cryosparc_P126_J4023_003_volume_map_half_A.mrc (#11) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998625 0.00523529 0.00031389 -0.97109463  
-0.00523523 0.99998627 -0.00021220 0.44237207  
-0.00031500 0.00021056 0.99999993 0.12645487  
Axis 0.04027075 0.05990654 -0.99739133  
Axis point 85.60249694 184.64779847 0.00000000  
Rotation angle (degrees) 0.30074416  
Shift along axis -0.13873071  
  

> fitmap #11 inMap #1

Fit map cryosparc_P126_J4023_003_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138113 points  
correlation = 0.9179, correlation about mean = 0.2458, overlap = 1.664e+04  
steps = 28, shift = 0.0171, angle = 0.0164 degrees  
  
Position of cryosparc_P126_J4023_003_volume_map_half_A.mrc (#11) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998502 0.00545441 0.00046410 -1.02505042  
-0.00545426 0.99998508 -0.00031696 0.50618634  
-0.00046583 0.00031443 0.99999984 0.13601178  
Axis 0.05757496 0.08479798 -0.99473334  
Axis point 94.64872752 186.59259606 0.00000000  
Rotation angle (degrees) 0.31416658  
Shift along axis -0.15138911  
  

> volume resample #11 #12 #10 onGrid #1

Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc resampled as #13, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc resampled as #14, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc resampled as #15, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4022_halfA_consensus_resampled.mrc #13

> save W20_J4022_halfB_consensus_resampled.mrc #14

> save W20_J4022_consensus_resampled.mrc #15

> close #10-15

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_consensus_resampled.mrc"

Opened W20_J4022_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  

> show #!8 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> close #8-10

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_005_volume_map_bprime_local.mrc"

Opened W20_J4022_005_volume_map_bprime_local.mrc as #8, grid size 240,240,240,
pixel 1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_A.mrc"

Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc as #9, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4022_005_volume_map_half_B.mrc"

Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc as #10, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  

> fitmap #8 inMap #1

Fit map W20_J4022_005_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure.mrc using 138200 points  
correlation = 0.9195, correlation about mean = 0.2263, overlap = 1.667e+04  
steps = 64, shift = 0.329, angle = 0.376 degrees  
  
Position of W20_J4022_005_volume_map_bprime_local.mrc (#8) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997966 0.00237299 0.00592048 -1.40324868  
-0.00238223 0.99999595 0.00155423 -0.17561136  
-0.00591677 -0.00156830 0.99998127 1.18884605  
Axis -0.23775685 0.90131776 -0.36207456  
Axis point 184.53246236 0.00000000 247.89429522  
Rotation angle (degrees) 0.37624341  
Shift along axis -0.25510056  
  

> fitmap #9 inMap #1

Fit map cryosparc_P126_J4022_005_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138165 points  
correlation = 0.9121, correlation about mean = 0.2433, overlap = 1.687e+04  
steps = 52, shift = 0.339, angle = 0.357 degrees  
  
Position of cryosparc_P126_J4022_005_volume_map_half_A.mrc (#9) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998304 0.00160770 0.00559706 -1.23594018  
-0.00161999 0.99999628 0.00219278 -0.39387001  
-0.00559351 -0.00220181 0.99998193 1.22871953  
Axis -0.35302911 0.89896616 -0.25928803  
Axis point 207.94947596 0.00000000 236.35689026  
Rotation angle (degrees) 0.35661877  
Shift along axis -0.23634521  
  

> fitmap #10 inMap #1

Fit map cryosparc_P126_J4022_005_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138076 points  
correlation = 0.9128, correlation about mean = 0.2508, overlap = 1.688e+04  
steps = 64, shift = 0.335, angle = 0.335 degrees  
  
Position of cryosparc_P126_J4022_005_volume_map_half_B.mrc (#10) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998354 0.00229208 0.00525924 -1.29178101  
-0.00229810 0.99999671 0.00113989 -0.13676617  
-0.00525661 -0.00115196 0.99998552 0.99455043  
Axis -0.19587427 0.89873969 -0.39230121  
Axis point 169.08755660 -0.00000000 255.83594172  
Rotation angle (degrees) 0.33520093  
Shift along axis -0.26005386  
  

> volume resample #8 #9 #10 onGrid #1

Opened W20_J4022_005_volume_map_bprime_local.mrc resampled as #11, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4022_005_volume_map_half_A.mrc resampled as #12, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4022_005_volume_map_half_B.mrc resampled as #13, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4022_halfA_consensus_resampled.mrc #12

> save W20_J4022_halfb_consensus_resampled.mrc #12

> save W20_J4022_halfB_consensus_resampled.mrc #12

> save W20_J4022_halfB_consensus_resampled.mrc #13

> save W20_J4022_halfA_consensus_resampled.mrc #12

> save W20_J4022_consensus_resampled.mrc #11

> close #8-10

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_consensus_resampled.mrc"

Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4022_halfB_consensus_resampled.mrc"

Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32  

> rename #9 J4022_half_maps

> close #11-13

> hide #!9 models

> hide #!8 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_A.mrc"

Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc as #10, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4023_003_volume_map_half_B.mrc"

Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc as #11, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_003_volume_map_bprime_local.mrc"

Opened W20_J4023_003_volume_map_bprime_local.mrc as #12, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> fitmap #10 inMap #1

Fit map cryosparc_P126_J4023_003_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138113 points  
correlation = 0.9179, correlation about mean = 0.2457, overlap = 1.663e+04  
steps = 52, shift = 0.377, angle = 0.301 degrees  
  
Position of cryosparc_P126_J4023_003_volume_map_half_A.mrc (#10) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998625 0.00523529 0.00031389 -0.97109463  
-0.00523523 0.99998627 -0.00021220 0.44237207  
-0.00031500 0.00021056 0.99999993 0.12645487  
Axis 0.04027075 0.05990654 -0.99739133  
Axis point 85.60249694 184.64779847 0.00000000  
Rotation angle (degrees) 0.30074416  
Shift along axis -0.13873071  
  

> fitmap #11 inMap #1

Fit map cryosparc_P126_J4023_003_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138029 points  
correlation = 0.9185, correlation about mean = 0.2483, overlap = 1.668e+04  
steps = 68, shift = 0.416, angle = 0.319 degrees  
  
Position of cryosparc_P126_J4023_003_volume_map_half_B.mrc (#11) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998492 0.00536357 0.00117882 -1.09568335  
-0.00536466 0.99998519 0.00091977 0.25675329  
-0.00117387 -0.00092608 0.99999888 0.47324489  
Axis -0.16573766 0.21124575 -0.96327891  
Axis point 55.94119463 211.23890617 0.00000000  
Rotation angle (degrees) 0.31905878  
Shift along axis -0.22003278  
  

> fitmap #12 inMap #1

Fit map W20_J4023_003_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure.mrc using 138098 points  
correlation = 0.9217, correlation about mean = 0.2228, overlap = 1.65e+04  
steps = 52, shift = 0.377, angle = 0.32 degrees  
  
Position of W20_J4023_003_volume_map_bprime_local.mrc (#12) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998445 0.00551741 0.00081396 -1.06075152  
-0.00551761 0.99998475 0.00023719 0.41218042  
-0.00081264 -0.00024168 0.99999964 0.27797318  
Axis -0.04289152 0.14569399 -0.98839950  
Axis point 78.63485140 193.79218176 0.00000000  
Rotation angle (degrees) 0.31984208  
Shift along axis -0.16919909  
  

> volume resample #11 #12 #10 onGrid #1

Opened cryosparc_P126_J4023_003_volume_map_half_B.mrc resampled as #13, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened W20_J4023_003_volume_map_bprime_local.mrc resampled as #14, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4023_003_volume_map_half_A.mrc resampled as #15, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4023_halfA_consensus_resampled.mrc #15

> save W20_J4023_halfB_consensus_resampled.mrc #13

> save W20_J4023_consensus_resampled.mrc #14

> close #10-12

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_consensus_resampled.mrc"

Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4023_halfB_consensus_resampled.mrc"

Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  

> rename #11 J4023_half_maps

> close #13-15

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4024_005_volume_map_half_B.mrc"

Opened cryosparc_P126_J4024_005_volume_map_half_B.mrc as #12, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4024_005_volume_map_half_A.mrc"

Opened cryosparc_P126_J4024_005_volume_map_half_A.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_005_volume_map_bprime_local.mrc"

Opened W20_J4024_005_volume_map_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  

> hide #!10 models

> hide #!11 models

> fitmap #12 inMap #1

Fit map cryosparc_P126_J4024_005_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138074 points  
correlation = 0.9152, correlation about mean = 0.3069, overlap = 1.694e+04  
steps = 48, shift = 0.275, angle = 0.182 degrees  
  
Position of cryosparc_P126_J4024_005_volume_map_half_B.mrc (#12) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999497 0.00227004 0.00221345 -0.56219185  
-0.00226948 0.99999739 -0.00025704 0.14204421  
-0.00221402 0.00025201 0.99999752 0.19043665  
Axis 0.08002006 0.69597786 -0.71359065  
Axis point 87.46071279 244.95972740 0.00000000  
Rotation angle (degrees) 0.18224416  
Shift along axis -0.08202081  
  

> fitmap #13 inMap #1

Fit map cryosparc_P126_J4024_005_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138160 points  
correlation = 0.9177, correlation about mean = 0.3098, overlap = 1.706e+04  
steps = 52, shift = 0.291, angle = 0.229 degrees  
  
Position of cryosparc_P126_J4024_005_volume_map_half_A.mrc (#13) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999333 0.00148868 0.00333575 -0.58679763  
-0.00149415 0.99999754 0.00163794 -0.27610320  
-0.00333331 -0.00164291 0.99999309 0.70324776  
Axis -0.40966600 0.83273727 -0.37245458  
Axis point 182.44969494 0.00000000 207.15832332  
Rotation angle (degrees) 0.22943002  
Shift along axis -0.25145824  
  

> fitmap #14 inMap #1

Fit map W20_J4024_005_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure.mrc using 138193 points  
correlation = 0.9249, correlation about mean = 0.3066, overlap = 1.679e+04  
steps = 64, shift = 0.289, angle = 0.207 degrees  
  
Position of W20_J4024_005_volume_map_bprime_local.mrc (#14) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999384 0.00210499 0.00280839 -0.61107104  
-0.00210740 0.99999741 0.00085537 -0.06363233  
-0.00280658 -0.00086128 0.99999569 0.47576775  
Axis -0.23755676 0.77702082 -0.58292833  
Axis point 131.43847496 0.00000000 233.23904124  
Rotation angle (degrees) 0.20701789  
Shift along axis -0.18161809  
  

> volume resample #13 #12 #14 onGrid #1

Opened cryosparc_P126_J4024_005_volume_map_half_A.mrc resampled as #15, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4024_005_volume_map_half_B.mrc resampled as #16, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened W20_J4024_005_volume_map_bprime_local.mrc resampled as #17, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4024_halfA_consensus_resampled.mrc #15

> save W20_J4024_halfB_consensus_resampled.mrc #16

> save W20_J4024_consensus_resampled.mrc #17

> combine #18

> hide #!28 models

> close #12-14

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_consensus_resampled.mrc"

Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4024_halfB_consensus_resampled.mrc"

Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32  

> rename #13 J4024_half_maps

> hide #!13 models

> hide #!12 models

> close #15-17

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_004_volume_map_bprime_local.mrc"

Opened W20_J4025_004_volume_map_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4025_004_volume_map_half_A.mrc"

Opened cryosparc_P126_J4025_004_volume_map_half_A.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4025_004_volume_map_half_B.mrc"

Opened cryosparc_P126_J4025_004_volume_map_half_B.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.262, step 1, values float32  

> fitmap #14 inMap #1

Fit map W20_J4025_004_volume_map_bprime_local.mrc in map
W20_J3623_consensus_structure.mrc using 138084 points  
correlation = 0.9112, correlation about mean = 0.1801, overlap = 1.617e+04  
steps = 56, shift = 0.729, angle = 0.309 degrees  
  
Position of W20_J4025_004_volume_map_bprime_local.mrc (#14) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999126 0.00417664 -0.00019252 -0.45232897  
-0.00417727 0.99998545 -0.00341415 0.60739960  
0.00017826 0.00341492 0.99999415 -0.09374688  
Axis 0.63253451 -0.03434313 -0.77377041  
Axis point 143.22381791 73.09529688 0.00000000  
Rotation angle (degrees) 0.30929457  
Shift along axis -0.23443512  
  

> fitmap #15 inMap #1

Fit map cryosparc_P126_J4025_004_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138098 points  
correlation = 0.9052, correlation about mean = 0.2004, overlap = 1.632e+04  
steps = 56, shift = 0.719, angle = 0.323 degrees  
  
Position of cryosparc_P126_J4025_004_volume_map_half_A.mrc (#15) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998806 0.00478731 -0.00097621 -0.44930386  
-0.00479005 0.99998454 -0.00282388 0.63846920  
0.00096268 0.00282852 0.99999554 -0.08426557  
Axis 0.50071333 -0.17175476 -0.84840230  
Axis point 123.64037299 66.63895829 0.00000000  
Rotation angle (degrees) 0.32339898  
Shift along axis -0.26314146  
  

> fitmap #16 inMap #1

Fit map cryosparc_P126_J4025_004_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138173 points  
correlation = 0.9079, correlation about mean = 0.2131, overlap = 1.642e+04  
steps = 52, shift = 0.742, angle = 0.262 degrees  
  
Position of cryosparc_P126_J4025_004_volume_map_half_B.mrc (#16) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999486 0.00315412 0.00057190 -0.38968890  
-0.00315224 0.99998971 -0.00326115 0.40412911  
-0.00058218 0.00325933 0.99999452 0.02235804  
Axis 0.71306302 0.12620638 -0.68964707  
Axis point 0.00000000 44.63041208 133.15812471  
Rotation angle (degrees) 0.26196640  
Shift along axis -0.24228822  
  

> volume resample #15 #16 #14 onGrid #1

Opened cryosparc_P126_J4025_004_volume_map_half_A.mrc resampled as #17, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4025_004_volume_map_half_B.mrc resampled as #41, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened W20_J4025_004_volume_map_bprime_local.mrc resampled as #90, grid size
240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4024_halfA_consensus_resampled.mrc #17

> hide #!13.2 models

> hide #!13.1 models

> show #!13.1 models

> hide #!13.1 models

> hide #!13 models

> hide #!41 models

> hide #!90 models

> show #!13.1 models

> hide #!13.1 models

> show #!13.1 models

> hide #!13.1 models

> show #!13.1 models

> hide #!13.1 models

> show #!13.2 models

> show #!13.1 models

> hide #!13.1 models

> hide #!13.2 models

> save W20_J4024_halfA_consensus_resampled.mrc #13.1

> save W20_J4025_halfA_consensus_resampled.mrc #17

> rename #17 W20_J4025_halfA_consensus_resampled.mrc

> show #!90 models

> show #!41 models

> save W20_J4025_halfB_consensus_resampled.mrc #41

> save W20_J4025_consensus_resampled.mrc #90

> hide #!13 models

> close #14-16

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_consensus_resampled.mrc"

Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  

> hide #!17 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4025_halfB_consensus_resampled.mrc"

Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> save W20_J4024_halfA_consensus_resampled.mrc #13.1

> rename #15 J4025_half_maps

> hide #!15 models

> hide #!14 models

> close #17

> close #18

> close #19

> close #20

> close #21

> close #22

> close #23

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4026_004_volume_map_half_A.mrc"

Opened cryosparc_P126_J4026_004_volume_map_half_A.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.266, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4026_004_volume_map_half_B.mrc"

Opened cryosparc_P126_J4026_004_volume_map_half_B.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.265, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_004_volume_map_gammazeta_local.mrc"

Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> hide #!41 models

> hide #!90 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> hide #!16 models

> show #!18 models

> hide #!18 models

> show #!18 models

> show #!17 models

> hide #!17 models

> show #!16 models

> hide #!16 models

> show #!16 models

> show #!17 models

> hide #!16 models

> show #!16 models

> hide #!17 models

> show #!17 models

> fitmap #16 inMap #1

Fit map cryosparc_P126_J4026_004_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138044 points  
correlation = 0.9061, correlation about mean = 0.2969, overlap = 1.877e+04  
steps = 52, shift = 0.633, angle = 0.336 degrees  
  
Position of cryosparc_P126_J4026_004_volume_map_half_A.mrc (#16) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999262 0.00086300 -0.00374493 -0.00440355  
-0.00084638 0.99998980 0.00443601 -0.04656357  
0.00374872 -0.00443280 0.99998315 0.35139305  
Axis -0.75569566 -0.63852116 -0.14565300  
Axis point 0.00000000 78.62510597 13.28594619  
Rotation angle (degrees) 0.33621225  
Shift along axis -0.01812188  
  

> fitmap #17 inMap #1

Fit map cryosparc_P126_J4026_004_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138078 points  
correlation = 0.906, correlation about mean = 0.2947, overlap = 1.874e+04  
steps = 56, shift = 0.632, angle = 0.326 degrees  
  
Position of cryosparc_P126_J4026_004_volume_map_half_B.mrc (#17) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999516 0.00097527 -0.00295606 -0.10060790  
-0.00096120 0.99998823 0.00475526 -0.05419298  
0.00296066 -0.00475240 0.99998432 0.51671634  
Axis -0.83660673 -0.52062903 -0.17039538  
Axis point 0.00000000 109.57038951 9.00298594  
Rotation angle (degrees) 0.32557225  
Shift along axis 0.02433761  
  

> fitmap #18 inMap #1

Fit map W20_J4026_004_volume_map_gammazeta_local.mrc in map
W20_J3623_consensus_structure.mrc using 138172 points  
correlation = 0.917, correlation about mean = 0.2905, overlap = 1.854e+04  
steps = 52, shift = 0.635, angle = 0.343 degrees  
  
Position of W20_J4026_004_volume_map_gammazeta_local.mrc (#18) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999273 0.00094755 -0.00369338 -0.01379933  
-0.00093047 0.99998888 0.00462325 -0.05119869  
0.00369772 -0.00461978 0.99998249 0.38867466  
Axis -0.77135465 -0.61680564 -0.15672526  
Axis point 0.00000000 83.44645675 13.76857176  
Rotation angle (degrees) 0.34328547  
Shift along axis -0.01869132  
  

> volume resample #17 #16 #18 onGrid #1

Opened cryosparc_P126_J4026_004_volume_map_half_B.mrc resampled as #19, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4026_004_volume_map_half_A.mrc resampled as #20, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened W20_J4026_004_volume_map_gammazeta_local.mrc resampled as #21, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4026_halfA_consensus_resampled.mrc #20

> save W20_J4026_halfB_consensus_resampled.mrc #19

> save W20_J4026_consensus_resampled.mrc #21

> close #16-18

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_consensus_resampled.mrc"

Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32  

> hide #!21 models

> hide #!20 models

> hide #!19 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4026_halfB_consensus_resampled.mrc"

Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> rename #17 J4026_half_maps

> close #19-21

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4027_005_volume_map_half_A.mrc"

Opened cryosparc_P126_J4027_005_volume_map_half_A.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4027_005_volume_map_half_B.mrc"

Opened cryosparc_P126_J4027_005_volume_map_half_B.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_005_volume_map_gammazeta_local.mrc"

Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  

> hide #!17 models

> hide #!16 models

> fitmap #18 inMap #1

Fit map cryosparc_P126_J4027_005_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138063 points  
correlation = 0.9242, correlation about mean = 0.4068, overlap = 1.895e+04  
steps = 64, shift = 0.865, angle = 0.418 degrees  
  
Position of cryosparc_P126_J4027_005_volume_map_half_A.mrc (#18) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997669 -0.00229559 0.00643030 -1.04477946  
0.00227893 0.99999403 0.00259782 -0.33276084  
-0.00643622 -0.00258311 0.99997595 1.91301880  
Axis -0.35472898 0.88094699 0.31320880  
Axis point 263.82795379 0.00000000 126.10679381  
Rotation angle (degrees) 0.41841556  
Shift along axis 0.67664322  
  

> fitmap #19 inMap #1

Fit map cryosparc_P126_J4027_005_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138195 points  
correlation = 0.9253, correlation about mean = 0.4118, overlap = 1.9e+04  
steps = 68, shift = 0.852, angle = 0.431 degrees  
  
Position of cryosparc_P126_J4027_005_volume_map_half_B.mrc (#19) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997498 -0.00277336 0.00650725 -0.98066980  
0.00275654 0.99999284 0.00259285 -0.39125472  
-0.00651439 -0.00257484 0.99997547 1.90493875  
Axis -0.34310644 0.86456626 0.36715549  
Axis point 252.66913251 0.00000000 114.89251767  
Rotation angle (degrees) 0.43148350  
Shift along axis 0.69761723  
  

> fitmap #20 inMap #1

Fit map W20_J4027_005_volume_map_gammazeta_local.mrc in map
W20_J3623_consensus_structure.mrc using 138160 points  
correlation = 0.9373, correlation about mean = 0.4299, overlap = 1.864e+04  
steps = 64, shift = 0.871, angle = 0.411 degrees  
  
Position of W20_J4027_005_volume_map_gammazeta_local.mrc (#20) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997680 -0.00234496 0.00639584 -1.04246365  
0.00233059 0.99999474 0.00225441 -0.28336984  
-0.00640109 -0.00223945 0.99997701 1.85486702  
Axis -0.31324184 0.89200052 0.32590584  
Axis point 254.76967129 0.00000000 130.69543046  
Rotation angle (degrees) 0.41099531  
Shift along axis 0.67828918  
  

> volume resample #19 #20 #18 onGrid #1

Opened cryosparc_P126_J4027_005_volume_map_half_B.mrc resampled as #21, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened W20_J4027_005_volume_map_gammazeta_local.mrc resampled as #22, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4027_005_volume_map_half_A.mrc resampled as #23, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4027_halfB_consensus_resampled.mrc #21

> save W20_J4027_halfA_consensus_resampled.mrc #23

> save W20_J4027_consensus_resampled.mrc #22

> close #18-20

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_consensus_resampled.mrc"

Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4027_halfB_consensus_resampled.mrc"

Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32  
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32  

> rename #19 J4017_half_maps

> rename #19 J4027_half_maps

> close #21-23

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4028_004_volume_map_half_A.mrc"

Opened cryosparc_P126_J4028_004_volume_map_half_A.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4028_004_volume_map_half_B.mrc"

Opened cryosparc_P126_J4028_004_volume_map_half_B.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_004_volume_map_gammazeta_local.mrc"

Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32  

> hide #!19 models

> hide #!18 models

> fitmap #20 inMap #1

Fit map cryosparc_P126_J4028_004_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138211 points  
correlation = 0.9192, correlation about mean = 0.3816, overlap = 1.899e+04  
steps = 52, shift = 0.522, angle = 0.296 degrees  
  
Position of cryosparc_P126_J4028_004_volume_map_half_A.mrc (#20) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998706 0.00198963 -0.00468116 0.25998221  
-0.00198544 0.99999762 0.00090051 0.55733772  
0.00468294 -0.00089120 0.99998864 -0.22070790  
Axis -0.17345663 -0.90654298 -0.38482804  
Axis point 85.46846238 0.00000000 38.05634596  
Rotation angle (degrees) 0.29591860  
Shift along axis -0.46541164  
  

> fitmap #21 inMap #1

Fit map cryosparc_P126_J4028_004_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138125 points  
correlation = 0.9186, correlation about mean = 0.3805, overlap = 1.898e+04  
steps = 48, shift = 0.516, angle = 0.21 degrees  
  
Position of cryosparc_P126_J4028_004_volume_map_half_B.mrc (#21) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999365 0.00064252 -0.00350470 0.30153938  
-0.00063949 0.99999942 0.00086460 0.34856397  
0.00350526 -0.00086235 0.99999348 -0.04103359  
Axis -0.23552090 -0.95601319 -0.17483906  
Axis point 31.62231369 0.00000000 59.29711678  
Rotation angle (degrees) 0.21006100  
Shift along axis -0.39707630  
  

> fitmap #22 inMap #1

Fit map W20_J4028_004_volume_map_gammazeta_local.mrc in map
W20_J3623_consensus_structure.mrc using 138218 points  
correlation = 0.9302, correlation about mean = 0.3927, overlap = 1.873e+04  
steps = 52, shift = 0.535, angle = 0.265 degrees  
  
Position of W20_J4028_004_volume_map_gammazeta_local.mrc (#22) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998992 0.00112578 -0.00434648 0.33637900  
-0.00112111 0.99999879 0.00107657 0.40418343  
0.00434769 -0.00107168 0.99998997 -0.12603288  
Axis -0.23266548 -0.94161994 -0.24334886  
Axis point 53.07995958 0.00000000 54.34764883  
Rotation angle (degrees) 0.26451275  
Shift along axis -0.42818100  
  

> volume resample #21 #20 #22 onGrid #1

Opened cryosparc_P126_J4028_004_volume_map_half_B.mrc resampled as #23, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J4028_004_volume_map_half_A.mrc resampled as #91, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened W20_J4028_004_volume_map_gammazeta_local.mrc resampled as #92, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J4028_halfA_consensus_resampled.mrc #91

> save W20_J4028_halfB_consensus_resampled.mrc #23

> save W20_J4028_consensus_resampled.mrc #92

> close #20-22

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_consensus_resampled.mrc"

Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J4028_halfB_consensus_resampled.mrc"

Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32  

> rename #21 J4028_half_maps

> combine #24

[Repeated 1 time(s)]

> close #22-24

> close #25

> close #26

> close #27

> hide #!93 models

> hide #!92 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3988_003_volume_map_half_A.mrc"

Opened cryosparc_P126_J3988_003_volume_map_half_A.mrc as #22, grid size
240,240,240, pixel 1.2, shown at level 0.291, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J3988_003_volume_map_half_B.mrc"

Opened cryosparc_P126_J3988_003_volume_map_half_B.mrc as #23, grid size
240,240,240, pixel 1.2, shown at level 0.291, step 1, values float32  

> select add #22

2 models selected  

> select add #23

4 models selected  

> hide #!21 models

> hide #!20 models

> ui mousemode right "rotate selected models"

> view matrix models
> #22,-0.85576,-0.11016,-0.5055,355.25,-0.33846,0.85818,0.38596,14.029,0.3913,0.50138,-0.77169,124.47,#23,-0.85576,-0.11016,-0.5055,355.25,-0.33846,0.85818,0.38596,14.029,0.3913,0.50138,-0.77169,124.47

> view matrix models
> #22,-0.53192,-0.84561,0.044824,336.27,-0.68771,0.46227,0.55979,96.534,-0.49408,0.26694,-0.82742,293.75,#23,-0.53192,-0.84561,0.044824,336.27,-0.68771,0.46227,0.55979,96.534,-0.49408,0.26694,-0.82742,293.75

> ui mousemode right "translate selected models"

> view matrix models
> #22,-0.53192,-0.84561,0.044824,335.35,-0.68771,0.46227,0.55979,94.798,-0.49408,0.26694,-0.82742,289.5,#23,-0.53192,-0.84561,0.044824,335.35,-0.68771,0.46227,0.55979,94.798,-0.49408,0.26694,-0.82742,289.5

> view matrix models
> #22,-0.53192,-0.84561,0.044824,337.81,-0.68771,0.46227,0.55979,89.918,-0.49408,0.26694,-0.82742,289.61,#23,-0.53192,-0.84561,0.044824,337.81,-0.68771,0.46227,0.55979,89.918,-0.49408,0.26694,-0.82742,289.61

> hide #!91 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc"

Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#24, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32  

> select add #24

6 models selected  

> select subtract #23

4 models selected  

> select subtract #22

2 models selected  

> view matrix models #24,1,0,0,4.4068,0,1,0,-1.5627,0,0,1,7.0623

> show #!1 models

> ui mousemode right "rotate selected models"

> view matrix models
> #24,-0.59721,0.29169,0.74717,82.383,0.43729,-0.66251,0.60816,89.121,0.6724,0.68993,0.2681,-83.296

> view matrix models
> #24,0.58998,-0.6462,-0.4841,224.91,-0.8066,-0.49879,-0.31719,374.29,-0.036497,0.57761,-0.8155,188.31

> view matrix models
> #24,-0.46477,-0.87473,-0.13728,358.04,-0.68335,0.25576,0.68383,105.04,-0.56305,0.41163,-0.71661,272.86

> fitmap #22 inMap #1

Fit map cryosparc_P126_J3988_003_volume_map_half_A.mrc in map
W20_J3623_consensus_structure.mrc using 138175 points  
correlation = 0.9519, correlation about mean = 0.5985, overlap = 2.143e+04  
steps = 320, shift = 8.89, angle = 19.2 degrees  
  
Position of cryosparc_P126_J3988_003_volume_map_half_A.mrc (#22) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33642694 -0.92057260 -0.19840110 353.49844057  
-0.77937135 0.15392648 0.60736063 147.09880294  
-0.52858037 0.35896062 -0.76925292 278.05341217  
Axis -0.56888343 0.75617354 0.32337782  
Axis point 252.39557005 0.00000000 81.74420969  
Rotation angle (degrees) 167.38948043  
Shift along axis 0.04912198  
  

> fitmap #23 inMap #1

Fit map cryosparc_P126_J3988_003_volume_map_half_B.mrc in map
W20_J3623_consensus_structure.mrc using 138208 points  
correlation = 0.9526, correlation about mean = 0.6, overlap = 2.142e+04  
steps = 324, shift = 8.99, angle = 19.2 degrees  
  
Position of cryosparc_P126_J3988_003_volume_map_half_B.mrc (#23) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33657596 -0.92064163 -0.19782722 353.45179614  
-0.77865335 0.15396136 0.60827203 146.98371640  
-0.52954280 0.35876857 -0.76868038 278.15909277  
Axis -0.56874816 0.75615237 0.32366516  
Axis point 252.42080897 0.00000000 81.66752530  
Rotation angle (degrees) 167.32947007  
Shift along axis 0.14743379  
  

> fitmap #24 inMap #1

Fit map
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc in
map W20_J3623_consensus_structure.mrc using 138204 points  
correlation = 0.9643, correlation about mean = 0.6577, overlap = 2.107e+04  
steps = 104, shift = 5.31, angle = 9.46 degrees  
  
Position of
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
(#24) relative to W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33645113 -0.92061038 -0.19818457 353.46943026  
-0.77924371 0.15400594 0.60750421 147.10114448  
-0.52875310 0.35882956 -0.76919534 278.08170115  
Axis -0.56885571 0.75619205 0.32338333  
Axis point 252.40251661 0.00000000 81.72856043  
Rotation angle (degrees) 167.37468234  
Shift along axis 0.09059859  
  

> select subtract #24

Nothing selected  

> volume resample #24 #23 #22 onGrid #1

Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc
resampled as #25, grid size 240,240,240, pixel 1.19, shown at step 1, values
float32  
Opened cryosparc_P126_J3988_003_volume_map_half_B.mrc resampled as #26, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  
Opened cryosparc_P126_J3988_003_volume_map_half_A.mrc resampled as #27, grid
size 240,240,240, pixel 1.19, shown at step 1, values float32  

> save W20_J3988_halfB_consensus_resampled.mrc #26

> save W20_J3988_halfA_consensus_resampled.mrc #27

> save W20_J3988_consensus_resampled.mrc #25

> close #22-24

> hide #!25 models

> hide #!26 models

> hide #!27 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_consensus_resampled.mrc"

Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_halfA_consensus_resampled.mrc"
> "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_halfB_consensus_resampled.mrc"

Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32  

> rename #23 J3988_half_maps

> close #25-27

> show #!28 models

> hide #!28 models

> rename #28 COPI_cyto_for_J4027_v1

> hide #!23 models

> hide #!22 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/LocalResolution_21/W20_J3623_consensus_structure_full.ccp4

Opened W20_J3623_consensus_structure_full.ccp4 as #24, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/LocalResolution_21/W20_J3623_consensus_structure_local_resolution.ccp4

Opened W20_J3623_consensus_structure_local_resolution.ccp4 as #25, grid size
240,240,240, pixel 1.19, shown at level 14, step 1, values float32  

> hide #!25 models

> show #!25 models

> hide #!25 models

> hide #!24 models

> show #!24 models

> hide #!1 models

> color sample #24 map #2 palette
> 2.0,purple:2.3,indigo:2.5,blue:2.8,cyan:3.0,lime:3.2, yellow:3.5,
> red:4.0,salmon:5.0,pink

Invalid "palette" argument: Missing color name or specifier  

> color sample #24 map #2

Map values for surface "surface": minimum -19.22, mean 2.61, maximum 22.06  

> close #24-25

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

> combine #27

No structures specified  

> combine #29

No structures specified  

> combine #28

> rename #24 COPI_cyto_for_J4027_v1

> split #24 chains

Split COPI_cyto_for_J4027_v1 (#24) into 13 models  
Chain information for COPI_cyto_for_J4027_v1 A #24.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 B #24.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 C #24.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 D #24.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 E #24.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 F #24.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 G #24.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 H #24.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 I #24.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 J #24.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 K #24.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 L #24.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_for_J4027_v1 M #24.13  
---  
Chain | Description  
M | No description available  
  

> show #!1 models

> color #1 darkgrey models

> color #1 #a9a9a9c0 models

> rename #24 COPI_cyto_J3623_model

> hide #!24 models

> show #!24 models

> hide #!1 models

> hide #!24 models

> combine #28

> split #25 chains

Split copy of COPI_cyto_for_J4027_v1 (#25) into 13 models  
Chain information for copy of COPI_cyto_for_J4027_v1 A #25.1  
---  
Chain | Description  
A | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 B #25.2  
---  
Chain | Description  
B | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 C #25.3  
---  
Chain | Description  
C | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 D #25.4  
---  
Chain | Description  
D | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 E #25.5  
---  
Chain | Description  
E | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 F #25.6  
---  
Chain | Description  
F | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 G #25.7  
---  
Chain | Description  
G | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 H #25.8  
---  
Chain | Description  
H | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 I #25.9  
---  
Chain | Description  
I | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 J #25.10  
---  
Chain | Description  
J | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 K #25.11  
---  
Chain | Description  
K | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 L #25.12  
---  
Chain | Description  
L | No description available  
  
Chain information for copy of COPI_cyto_for_J4027_v1 M #25.13  
---  
Chain | Description  
M | No description available  
  

> show #!4 models

> rename #25 COPI_cyto_for_J4027_v1

> rename #25 COPI_cyto_J3987_model

> fitmap #25.1 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 A (#25.1) to map
W20_J3987_consensus_resampled.mrc (#4) using 2590 atoms  
average map value = 0.3221, steps = 104  
shifted from previous position = 0.721  
rotated from previous position = 1.24 degrees  
atoms outside contour = 795, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 A (#25.1) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.38689637 -0.90569538 -0.17328327 278.18188435  
-0.79467842 0.23216071 0.56088111 163.52034472  
-0.46775786 0.35470734 -0.80955871 239.74100561  
Axis -0.54800188 0.78270203 0.29507876  
Axis point 210.04111237 0.00000000 70.64408205  
Rotation angle (degrees) 169.15725379  
Shift along axis 46.28598736  
  

> fitmap #25.2 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 B (#25.2) to map
W20_J3987_consensus_resampled.mrc (#4) using 2426 atoms  
average map value = 0.3153, steps = 72  
shifted from previous position = 0.757  
rotated from previous position = 2.26 degrees  
atoms outside contour = 839, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 B (#25.2) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.39471401 -0.89888974 -0.19025799 280.36384015  
-0.79142130 0.22743083 0.56738660 162.69216971  
-0.46674746 0.37452966 -0.80117062 238.28935068  
Axis -0.54506838 0.78143761 0.30373627  
Axis point 209.70723896 0.00000000 70.08028018  
Rotation angle (degrees) 169.81012722  
Shift along axis 46.69343412  
  

> fitmap #25.3 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 C (#25.3) to map
W20_J3987_consensus_resampled.mrc (#4) using 1612 atoms  
average map value = 0.3176, steps = 56  
shifted from previous position = 0.728  
rotated from previous position = 2.04 degrees  
atoms outside contour = 641, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 C (#25.3) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.39605343 -0.89988782 -0.18260232 278.68660008  
-0.79444663 0.23610267 0.55956242 163.22266002  
-0.46043050 0.36668441 -0.80842211 238.93411170  
Axis -0.54443563 0.78422400 0.29762824  
Axis point 208.79769571 0.00000000 71.16300785  
Rotation angle (degrees) 169.79703161  
Shift along axis 47.38975067  
  

> fitmap #25.4 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 D (#25.4) to map
W20_J3987_consensus_resampled.mrc (#4) using 4745 atoms  
average map value = 0.3393, steps = 64  
shifted from previous position = 0.197  
rotated from previous position = 0.999 degrees  
atoms outside contour = 1721, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 D (#25.4) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.36755215 -0.91697806 -0.15510211 274.92468941  
-0.80291601 0.22872446 0.55046437 165.41983596  
-0.46928810 0.32685833 -0.82032452 243.67714165  
Axis -0.55602986 0.78127043 0.28363236  
Axis point 211.32871948 0.00000000 72.29578138  
Rotation angle (degrees) 168.40024254  
Shift along axis 45.48601304  
  

> fitmap #25.5 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 E (#25.5) to map
W20_J3987_consensus_resampled.mrc (#4) using 1876 atoms  
average map value = 0.3141, steps = 48  
shifted from previous position = 0.53  
rotated from previous position = 0.888 degrees  
atoms outside contour = 674, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 E (#25.5) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.38334136 -0.90913799 -0.16284208 277.17803202  
-0.79171318 0.23265338 0.56485632 162.82482750  
-0.47564657 0.34545700 -0.80896218 242.10131222  
Axis -0.54889072 0.78257074 0.29377205  
Axis point 210.42677765 0.00000000 70.96904172  
Rotation angle (degrees) 168.47140268  
Shift along axis 46.40409379  
  

> fitmap #25.6 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 F (#25.6) to map
W20_J3987_consensus_resampled.mrc (#4) using 2400 atoms  
average map value = 0.2626, steps = 84  
shifted from previous position = 2.71  
rotated from previous position = 2.99 degrees  
atoms outside contour = 1310, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 F (#25.6) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.40199255 -0.90304968 -0.15133829 274.52161881  
-0.76596507 0.24109454 0.59596221 157.65702153  
-0.50169664 0.35549220 -0.78862272 240.80158217  
Axis -0.53855753 0.78466390 0.30701522  
Axis point 207.61107533 0.00000000 67.84938526  
Rotation angle (degrees) 167.09978512  
Shift along axis 49.79183984  
  

> fitmap #25.7 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 G (#25.7) to map
W20_J3987_consensus_resampled.mrc (#4) using 2302 atoms  
average map value = 0.2759, steps = 60  
shifted from previous position = 1.78  
rotated from previous position = 1.99 degrees  
atoms outside contour = 1124, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 G (#25.7) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.37472415 -0.90717861 -0.19133425 277.62448174  
-0.79104565 0.20520230 0.57631485 166.08473990  
-0.48355827 0.36731321 -0.79451395 238.83413932  
Axis -0.55353568 0.77394812 0.30757528  
Axis point 211.98709934 0.00000000 67.68536340  
Rotation angle (degrees) 169.11794633  
Shift along axis 48.32539250  
  

> fitmap #25.8 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 H (#25.8) to map
W20_J3987_consensus_resampled.mrc (#4) using 420 atoms  
average map value = 0.339, steps = 56  
shifted from previous position = 1.73  
rotated from previous position = 4.37 degrees  
atoms outside contour = 139, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 H (#25.8) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.30262332 -0.93808653 -0.16856100 274.79297984  
-0.83162161 0.17348487 0.52754953 176.28282750  
-0.46564432 0.29982776 -0.83263359 248.60795718  
Axis -0.58515271 0.76338380 0.27357170  
Axis point 220.21870033 0.00000000 73.46391590  
Rotation angle (degrees) 168.77962388  
Shift along axis 41.78769794  
  

> fitmap #25.9 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 I (#25.9) to map
W20_J3987_consensus_resampled.mrc (#4) using 1573 atoms  
average map value = 0.3297, steps = 60  
shifted from previous position = 0.384  
rotated from previous position = 0.597 degrees  
atoms outside contour = 540, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 I (#25.9) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.37451788 -0.91088738 -0.17326443 276.29637371  
-0.79727848 0.22096017 0.56171491 164.46884657  
-0.47337448 0.34851227 -0.80898443 241.62397254  
Axis -0.55339354 0.77897237 0.29488579  
Axis point 210.79260550 0.00000000 70.83395311  
Rotation angle (degrees) 168.89357390  
Shift along axis 46.46753453  
  

> fitmap #25.10 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 J (#25.10) to map
W20_J3987_consensus_resampled.mrc (#4) using 1112 atoms  
average map value = 0.3174, steps = 56  
shifted from previous position = 0.808  
rotated from previous position = 4.24 degrees  
atoms outside contour = 445, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 J (#25.10) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.37184146 -0.92295368 -0.09945074 269.60235343  
-0.79986239 0.26418072 0.53891439 164.53018199  
-0.47112005 0.27993762 -0.83646927 249.12759996  
Axis -0.55169100 0.79175677 0.26221794  
Axis point 209.92414105 0.00000000 75.11235729  
Rotation angle (degrees) 166.42536541  
Shift along axis 46.85641909  
  

> fitmap #25.11 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 K (#25.11) to map
W20_J3987_consensus_resampled.mrc (#4) using 319 atoms  
average map value = 0.3247, steps = 356  
shifted from previous position = 18  
rotated from previous position = 29.8 degrees  
atoms outside contour = 122, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 K (#25.11) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.11497818 -0.99056474 0.07457564 250.16493380  
-0.55287660 0.12618381 0.82365352 113.16758699  
-0.82529237 0.05347106 -0.56216845 259.79352847  
Axis -0.60992918 0.71263081 0.34661756  
Axis point 236.76411941 0.00000000 37.20193482  
Rotation angle (degrees) 140.84869902  
Shift along axis 18.11281583  
  

> fitmap #25.12 inMap #4

Fit molecule copy of COPI_cyto_for_J4027_v1 L (#25.12) to map
W20_J3987_consensus_resampled.mrc (#4) using 1420 atoms  
average map value = 0.2216, steps = 244  
shifted from previous position = 20  
rotated from previous position = 43.1 degrees  
atoms outside contour = 1209, contour level = 0.27665  
  
Position of copy of COPI_cyto_for_J4027_v1 L (#25.12) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.33704271 -0.93889900 0.06979181 244.25606438  
-0.21172527 0.14781713 0.96608619 12.69558044  
-0.91737377 0.31083561 -0.24860932 233.11919004  
Axis -0.47133855 0.71009352 0.52307472  
Axis point 190.36197930 0.00000000 40.21086330  
Rotation angle (degrees) 135.96517505  
Shift along axis 15.82650607  
  

> close #25

> combine #28

> color #4 darkgrey models

> color #4 #a9a9a9bf models

> rename #25 COPI_cyto_J3987_model

> fitmap #25 inMap #4

Fit molecule COPI_cyto_J3987_model (#25) to map
W20_J3987_consensus_resampled.mrc (#4) using 27347 atoms  
average map value = 0.2864, steps = 40  
shifted from previous position = 0.228  
rotated from previous position = 0.219 degrees  
atoms outside contour = 13455, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model (#25) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.37179442 -0.91394156 -0.16272598 275.88087564  
-0.79687792 0.22429417 0.56096143 164.32455600  
-0.47618747 0.33823507 -0.81169116 242.44716299  
Axis -0.55410562 0.77983932 0.29123460  
Axis point 211.23166983 0.00000000 70.92651391  
Rotation angle (degrees) 168.40582967  
Shift along axis 45.88860967  
  

> hide #!25 models

> show #!24 models

> combine #28

> hide #!4 models

> show #!6 models

> color #6 darkgrey models

> color #6 #a9a9a9bf models

> fitmap #26 inMap #6

Fit molecule copy of COPI_cyto_for_J4027_v1 (#26) to map
W20_J4021_consensus_resampled.mrc (#6) using 27347 atoms  
average map value = 0.2574, steps = 88  
shifted from previous position = 0.804  
rotated from previous position = 1.33 degrees  
atoms outside contour = 13999, contour level = 0.25941  
  
Position of copy of COPI_cyto_for_J4027_v1 (#26) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.39044300 -0.90597356 -0.16360374 277.32294036  
-0.78887242 0.23762979 0.56675603 162.18357201  
-0.47458885 0.35034840 -0.80747844 241.34338581  
Axis -0.54571767 0.78421483 0.29529532  
Axis point 209.61127190 0.00000000 70.79010036  
Rotation angle (degrees) 168.56372015  
Shift along axis 47.11430470  
  

> rename #26 COPI_cyto_J4021_model

> hide #!26 models

> combine #28

> close #29-33

> rename #27 COPI_cyto_J4022_model

> rename #28 COPI_cyto_J4023_model

> combine #28

> hide #!27 models

> hide #!24 models

> rename #29 COPI_cyto_J4024_model

> combine #29

[Repeated 1 time(s)]

> rename #30 COPI_cyto_J4025_model

> rename #31 COPI_cyto_J4026_model

> combine #29

> rename #32 COPI_cyto_J4027_model

> combine #29

> rename #33 COPI_cyto_J4028_model

> hide #!29 models

> hide #!30 models

> hide #!31 models

> hide #!32 models

> hide #!33 models

> combine #29

> close #35-36,39#34,37-38

> combine #29

> rename #34 COPI_cyto_J3988_model

> hide #!34 models

> close #40

> close #41

> close #42-46

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!1 models

> fitmap #24.1 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 A (#24.1) to map
W20_J3623_consensus_structure.mrc (#1) using 2590 atoms  
average map value = 0.3549, steps = 116  
shifted from previous position = 0.529  
rotated from previous position = 1.66 degrees  
atoms outside contour = 606, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 A (#24.1) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.39542896 -0.90304867 -0.16774700 278.17983361  
-0.78821131 0.23986960 0.56673233 161.55778287  
-0.47154946 0.35632245 -0.80664455 240.52362588  
Axis -0.54371860 0.78505369 0.29675038  
Axis point 209.13140963 0.00000000 70.83505847  
Rotation angle (degrees) 168.84338449  
Shift along axis 46.95546224  
  

> fitmap #24.2 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 B (#24.2) to map
W20_J3623_consensus_structure.mrc (#1) using 2426 atoms  
average map value = 0.3443, steps = 84  
shifted from previous position = 1.05  
rotated from previous position = 2.23 degrees  
atoms outside contour = 613, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 B (#24.2) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.39499091 -0.89904452 -0.18894748 279.87559115  
-0.79097752 0.22820260 0.56769548 163.08646468  
-0.46726520 0.37368776 -0.80126194 238.60471247  
Axis -0.54487475 0.78166114 0.30350844  
Axis point 209.64905720 0.00000000 70.09351394  
Rotation angle (degrees) 169.74498652  
Shift along axis 47.39975428  
  

> fitmap #24.3 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 C (#24.3) to map
W20_J3623_consensus_structure.mrc (#1) using 1612 atoms  
average map value = 0.3398, steps = 68  
shifted from previous position = 0.582  
rotated from previous position = 1.57 degrees  
atoms outside contour = 545, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 C (#24.3) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.38289473 -0.90536973 -0.18356823 277.48749747  
-0.80205073 0.22720768 0.55235071 164.98384273  
-0.45837350 0.35872321 -0.81314907 239.04481293  
Axis -0.55056634 0.78138966 0.29378038  
Axis point 209.64934014 0.00000000 71.32622789  
Rotation angle (degrees) 169.87222630  
Shift along axis 46.36806823  
  

> fitmap #24.4 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 D (#24.4) to map
W20_J3623_consensus_structure.mrc (#1) using 4745 atoms  
average map value = 0.3686, steps = 104  
shifted from previous position = 0.253  
rotated from previous position = 1.26 degrees  
atoms outside contour = 1389, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 D (#24.4) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.36437524 -0.91895662 -0.15082912 274.51036554  
-0.80384056 0.22859535 0.54916713 165.68273324  
-0.47018193 0.32134547 -0.82198909 244.27756191  
Axis -0.55725502 0.78114152 0.28157552  
Axis point 211.66245571 0.00000000 72.46008698  
Rotation angle (degrees) 168.20479189  
Shift along axis 45.23196284  
  

> fitmap #24.5 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 E (#24.5) to map
W20_J3623_consensus_structure.mrc (#1) using 1876 atoms  
average map value = 0.352, steps = 52  
shifted from previous position = 0.551  
rotated from previous position = 2.49 degrees  
atoms outside contour = 518, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 E (#24.5) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.40106793 -0.89989636 -0.17126318 279.30609803  
-0.77603258 0.23443438 0.58550318 159.37835572  
-0.48674220 0.36773235 -0.79237300 240.44712243  
Axis -0.54056671 0.78310515 0.30746375  
Axis point 209.32932986 0.00000000 69.11212793  
Rotation angle (degrees) 168.37950772  
Shift along axis 47.75520439  
  

> fitmap #24.6 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 F (#24.6) to map
W20_J3623_consensus_structure.mrc (#1) using 2400 atoms  
average map value = 0.1995, steps = 32  
shifted from previous position = 0.88  
rotated from previous position = 2.72 degrees  
atoms outside contour = 2236, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 F (#24.6) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.34705513 -0.92807037 -0.13504869 272.53895474  
-0.78593629 0.20923862 0.58182761 162.32498204  
-0.51171956 0.30806592 -0.80202151 247.95535590  
Axis -0.56230557 0.77368067 0.29194291  
Axis point 214.01677259 0.00000000 69.57811076  
Rotation angle (degrees) 165.91105545  
Shift along axis 44.72633565  
  

> fitmap #24.7 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 G (#24.7) to map
W20_J3623_consensus_structure.mrc (#1) using 2302 atoms  
average map value = 0.2042, steps = 56  
shifted from previous position = 0.732  
rotated from previous position = 2.42 degrees  
atoms outside contour = 1956, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 G (#24.7) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.40089736 -0.90460310 -0.14482596 274.53357578  
-0.79035024 0.26156664 0.55401210 159.12795064  
-0.46327942 0.33656522 -0.81981464 242.17863151  
Axis -0.54066936 0.79181649 0.28408325  
Axis point 206.28449602 0.00000000 73.32567888  
Rotation angle (degrees) 168.39926749  
Shift along axis 46.36713644  
  

> fitmap #24.8 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 H (#24.8) to map
W20_J3623_consensus_structure.mrc (#1) using 420 atoms  
average map value = 0.2665, steps = 72  
shifted from previous position = 1.63  
rotated from previous position = 6.63 degrees  
atoms outside contour = 172, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 H (#24.8) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.32134690 -0.93539737 -0.14753964 274.57265625  
-0.85481390 0.21949425 0.47022919 174.99288921  
-0.40746704 0.27722563 -0.87012446 247.94129870  
Axis -0.57850272 0.77909809 0.24153833  
Axis point 215.13355776 0.00000000 80.87806975  
Rotation angle (degrees) 170.39742774  
Shift along axis 37.38292387  
  

> fitmap #24.9 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 I (#24.9) to map
W20_J3623_consensus_structure.mrc (#1) using 1573 atoms  
average map value = 0.3464, steps = 64  
shifted from previous position = 0.478  
rotated from previous position = 0.943 degrees  
atoms outside contour = 463, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 I (#24.9) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.36293127 -0.91488242 -0.17683625 275.64058476  
-0.80647349 0.21333854 0.55144102 166.30863857  
-0.46677771 0.34274894 -0.81525564 240.90103613  
Axis -0.55901039 0.77664797 0.29038821  
Axis point 211.48290973 0.00000000 71.12426755  
Rotation angle (degrees) 169.24194914  
Shift along axis 45.03213770  
  

> fitmap #24.10 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 J (#24.10) to map
W20_J3623_consensus_structure.mrc (#1) using 1112 atoms  
average map value = 0.3459, steps = 52  
shifted from previous position = 0.38  
rotated from previous position = 3.4 degrees  
atoms outside contour = 351, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 J (#24.10) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.36982106 -0.92265040 -0.10930983 270.39934908  
-0.79564879 0.25374928 0.55004938 163.22079540  
-0.47976598 0.29039208 -0.82794750 248.56734521  
Axis -0.55260110 0.78840254 0.27028405  
Axis point 210.23381150 0.00000000 73.93598950  
Rotation angle (degrees) 166.41185550  
Shift along axis 46.44450154  
  

> fitmap #24.11 inMap #1

Fit molecule COPI_cyto_for_J4027_v1 K (#24.11) to map
W20_J3623_consensus_structure.mrc (#1) using 319 atoms  
average map value = 0.2981, steps = 324  
shifted from previous position = 19.5  
rotated from previous position = 32.5 degrees  
atoms outside contour = 138, contour level = 0.25746  
  
Position of COPI_cyto_for_J4027_v1 K (#24.11) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.06351642 -0.99614584 0.06049082 250.07246282  
-0.53379297 0.08512482 0.84131971 112.08368631  
-0.84322639 0.02114804 -0.53714247 260.93738590  
Axis -0.62845977 0.69247687 0.35427971  
Axis point 244.61405927 0.00000000 32.59441219  
Rotation angle (degrees) 139.26773764  
Shift along axis 12.89969989  
  

> split #25 chains

Split COPI_cyto_J3987_model (#25) into 13 models  
Chain information for COPI_cyto_J3987_model A #25.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J3987_model B #25.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J3987_model C #25.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J3987_model D #25.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J3987_model E #25.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J3987_model F #25.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J3987_model G #25.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J3987_model H #25.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J3987_model I #25.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J3987_model J #25.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J3987_model K #25.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J3987_model L #25.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J3987_model M #25.13  
---  
Chain | Description  
M | No description available  
  

> hide #!1 models

> show #!4 models

> fitmap #25.1 inMap #4

Fit molecule COPI_cyto_J3987_model A (#25.1) to map
W20_J3987_consensus_resampled.mrc (#4) using 2590 atoms  
average map value = 0.3221, steps = 80  
shifted from previous position = 0.776  
rotated from previous position = 1.16 degrees  
atoms outside contour = 793, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model A (#25.1) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.38698629 -0.90565681 -0.17328409 278.18136001  
-0.79448095 0.23210684 0.56118308 163.47572576  
-0.46801885 0.35484106 -0.80934924 239.73459315  
Axis -0.54794991 0.78268057 0.29523216  
Axis point 210.03344096 0.00000000 70.61465245  
Rotation angle (degrees) 169.14725684  
Shift along axis 46.29718384  
  

> fitmap #25.2 inMap #4

Fit molecule COPI_cyto_J3987_model B (#25.2) to map
W20_J3987_consensus_resampled.mrc (#4) using 2426 atoms  
average map value = 0.3153, steps = 72  
shifted from previous position = 0.76  
rotated from previous position = 2.24 degrees  
atoms outside contour = 837, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model B (#25.2) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.39446310 -0.89902146 -0.19015597 280.33015308  
-0.79147162 0.22726378 0.56738336 162.70699196  
-0.46687424 0.37431485 -0.80119714 238.32585966  
Axis -0.54517505 0.78138014 0.30369267  
Axis point 209.72584131 0.00000000 70.08251673  
Rotation angle (degrees) 169.80084660  
Shift along axis 46.68482501  
  

> fitmap #25.3 inMap #4

Fit molecule COPI_cyto_J3987_model C (#25.3) to map
W20_J3987_consensus_resampled.mrc (#4) using 1612 atoms  
average map value = 0.3176, steps = 88  
shifted from previous position = 0.713  
rotated from previous position = 1.99 degrees  
atoms outside contour = 638, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model C (#25.3) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.39593352 -0.89983916 -0.18310146 278.71276949  
-0.79448375 0.23569092 0.55968328 163.24766694  
-0.46046958 0.36706850 -0.80822553 238.88829135  
Axis -0.54450663 0.78409758 0.29783135  
Axis point 208.81546281 0.00000000 71.13107453  
Rotation angle (degrees) 169.81244748  
Shift along axis 47.38957070  
  

> fitmap #25.4 inMap #4

Fit molecule COPI_cyto_J3987_model D (#25.4) to map
W20_J3987_consensus_resampled.mrc (#4) using 4745 atoms  
average map value = 0.3393, steps = 64  
shifted from previous position = 0.187  
rotated from previous position = 0.91 degrees  
atoms outside contour = 1720, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model D (#25.4) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.36779496 -0.91688768 -0.15506087 274.91861534  
-0.80287248 0.22897373 0.55042423 165.38152260  
-0.46917233 0.32693736 -0.82035926 243.65468775  
Axis -0.55592398 0.78135279 0.28361301  
Axis point 211.28631778 0.00000000 72.30612718  
Rotation angle (degrees) 168.40427173  
Shift along axis 45.49110059  
  

> hide #!95 models

> show #25.1 models

> show #25.2 models

> show #25.3 models

> show #!25.4 models

> show #25.5 models

> show #25.6 models

> show #25.7 models

> show #25.8 models

> show #25.9 models

> show #25.10 models

> show #25.11 models

> show #25.12 models

> show #25.13 models

> fitmap #25.5 inMap #4

Fit molecule COPI_cyto_J3987_model E (#25.5) to map
W20_J3987_consensus_resampled.mrc (#4) using 1876 atoms  
average map value = 0.3141, steps = 60  
shifted from previous position = 0.493  
rotated from previous position = 0.732 degrees  
atoms outside contour = 674, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model E (#25.5) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.38331200 -0.90908551 -0.16320372 277.20038029  
-0.79186725 0.23250965 0.56469952 162.86818551  
-0.47541371 0.34569178 -0.80899877 242.05560365  
Axis -0.54892849 0.78253380 0.29379988  
Axis point 210.42960898 0.00000000 70.96821393  
Rotation angle (degrees) 168.49306276  
Shift along axis 46.40258047  
  

> fitmap #25.6 inMap #4

Fit molecule COPI_cyto_J3987_model F (#25.6) to map
W20_J3987_consensus_resampled.mrc (#4) using 2400 atoms  
average map value = 0.2626, steps = 52  
shifted from previous position = 2.64  
rotated from previous position = 2.91 degrees  
atoms outside contour = 1308, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model F (#25.6) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.40208359 -0.90303670 -0.15117378 274.51102549  
-0.76578539 0.24117028 0.59616243 157.61497455  
-0.50189793 0.35547381 -0.78850292 240.80443864  
Axis -0.53849728 0.78468186 0.30707499  
Axis point 207.60053656 0.00000000 67.83219255  
Rotation angle (degrees) 167.08638464  
Shift along axis 49.79919045  
  

> fitmap #25.7 inMap #4

Fit molecule COPI_cyto_J3987_model G (#25.7) to map
W20_J3987_consensus_resampled.mrc (#4) using 2302 atoms  
average map value = 0.2759, steps = 68  
shifted from previous position = 1.66  
rotated from previous position = 2.11 degrees  
atoms outside contour = 1125, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model G (#25.7) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.37470678 -0.90717007 -0.19140875 277.62743359  
-0.79108106 0.20516374 0.57627998 166.08595678  
-0.48351381 0.36735586 -0.79452130 238.82922597  
Axis -0.55354811 0.77393742 0.30757985  
Axis point 211.98563964 0.00000000 67.68895792  
Rotation angle (degrees) 169.12227850  
Shift along axis 48.31905400  
  

> fitmap #25.8 inMap #4

Fit molecule COPI_cyto_J3987_model H (#25.8) to map
W20_J3987_consensus_resampled.mrc (#4) using 420 atoms  
average map value = 0.3391, steps = 52  
shifted from previous position = 1.47  
rotated from previous position = 4.51 degrees  
atoms outside contour = 138, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model H (#25.8) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.30273203 -0.93833428 -0.16697938 274.74649750  
-0.83167276 0.17451603 0.52712864 176.16874621  
-0.46548229 0.29845092 -0.83321864 248.80226785  
Axis -0.58505795 0.76370144 0.27288698  
Axis point 220.19027093 0.00000000 73.60291153  
Rotation angle (degrees) 168.73005781  
Shift along axis 41.69260200  
  

> fitmap #25.9 inMap #4

Fit molecule COPI_cyto_J3987_model I (#25.9) to map
W20_J3987_consensus_resampled.mrc (#4) using 1573 atoms  
average map value = 0.3297, steps = 60  
shifted from previous position = 0.422  
rotated from previous position = 0.637 degrees  
atoms outside contour = 541, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model I (#25.9) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.37486313 -0.91082017 -0.17287068 276.29172892  
-0.79723061 0.22153165 0.56155775 164.41773716  
-0.47318179 0.34832509 -0.80917775 241.63479140  
Axis -0.55323087 0.77915540 0.29470744  
Axis point 210.74543880 0.00000000 70.87207510  
Rotation angle (degrees) 168.88868220  
Shift along axis 46.46542504  
  

> fitmap #25.10 inMap #4

Fit molecule COPI_cyto_J3987_model J (#25.10) to map
W20_J3987_consensus_resampled.mrc (#4) using 1112 atoms  
average map value = 0.3174, steps = 68  
shifted from previous position = 0.699  
rotated from previous position = 4.11 degrees  
atoms outside contour = 446, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model J (#25.10) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.37167949 -0.92301396 -0.09949677 269.60077643  
-0.80025326 0.26421818 0.53831543 164.62224104  
-0.47058379 0.27970342 -0.83684940 249.14141931  
Axis -0.55179431 0.79177956 0.26193160  
Axis point 209.93718651 0.00000000 75.17215989  
Rotation angle (degrees) 166.44743618  
Shift along axis 46.83836222  
  

> fitmap #25.11 inMap #4

Fit molecule COPI_cyto_J3987_model K (#25.11) to map
W20_J3987_consensus_resampled.mrc (#4) using 319 atoms  
average map value = 0.3247, steps = 352  
shifted from previous position = 17.9  
rotated from previous position = 29.5 degrees  
atoms outside contour = 122, contour level = 0.27665  
  
Position of COPI_cyto_J3987_model K (#25.11) relative to
W20_J3987_consensus_resampled.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.11943694 -0.99009806 0.07376081 250.46546690  
-0.55633477 0.12827455 0.82099774 113.52890835  
-0.82232990 0.05702176 -0.56614669 259.81159734  
Axis -0.60879152 0.71407012 0.34565408  
Axis point 236.23455332 0.00000000 37.79456885  
Rotation angle (degrees) 141.13755065  
Shift along axis 18.39128867  
  

> select add #25.11

319 atoms, 320 bonds, 37 residues, 1 model selected  

> view matrix models
> #25.11,-0.13737,-0.98867,0.060447,253.17,-0.58792,0.1305,0.79832,118.22,-0.79717,0.074131,-0.59919,261.16

> ui tool show Matchmaker

> matchmaker #25.11 to #26

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_cyto_J4021_model, chain K (#26) with COPI_cyto_J3987_model K,
chain K (#25.11), sequence alignment score = 192.1  
RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
0.000)  
  

> select subtract #25.11

Nothing selected  

> hide #!25 models

> show #!26 models

> split #26 chains

Split COPI_cyto_J4021_model (#26) into 13 models  
Chain information for COPI_cyto_J4021_model A #26.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4021_model B #26.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4021_model C #26.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4021_model D #26.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4021_model E #26.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4021_model F #26.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4021_model G #26.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4021_model H #26.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4021_model I #26.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4021_model J #26.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4021_model K #26.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4021_model L #26.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4021_model M #26.13  
---  
Chain | Description  
M | No description available  
  

> hide #!4 models

> show #!6 models

> fitmap #26.1 inMap #6

Fit molecule COPI_cyto_J4021_model A (#26.1) to map
W20_J4021_consensus_resampled.mrc (#6) using 2590 atoms  
average map value = 0.2703, steps = 84  
shifted from previous position = 0.378  
rotated from previous position = 1.1 degrees  
atoms outside contour = 937, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model A (#26.1) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.37414892 -0.91220652 -0.16700861 276.47462167  
-0.79157778 0.22032122 0.56996772 162.80224157  
-0.48313272 0.34545310 -0.80451534 242.25699208  
Axis -0.55289681 0.77849727 0.29706416  
Axis point 211.11351512 0.00000000 70.18074399  
Rotation angle (degrees) 168.28551633  
Shift along axis 45.84503360  
  

> fitmap #26.2 inMap #6

Fit molecule COPI_cyto_J4021_model B (#26.2) to map
W20_J4021_consensus_resampled.mrc (#6) using 2426 atoms  
average map value = 0.2468, steps = 64  
shifted from previous position = 0.762  
rotated from previous position = 1.85 degrees  
atoms outside contour = 1379, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model B (#26.2) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.37049992 -0.90946831 -0.18867225 277.51418546  
-0.80121018 0.21016989 0.56025966 165.92440083  
-0.46988517 0.35874228 -0.80654319 240.14558920  
Axis -0.55590253 0.77574936 0.29863910  
Axis point 211.54042372 0.00000000 70.27796042  
Rotation angle (degrees) 169.55728062  
Shift along axis 46.16177391  
  

> fitmap #26.3 inMap #6

Fit molecule COPI_cyto_J4021_model C (#26.3) to map
W20_J4021_consensus_resampled.mrc (#6) using 1612 atoms  
average map value = 0.268, steps = 88  
shifted from previous position = 1.42  
rotated from previous position = 8.83 degrees  
atoms outside contour = 658, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model C (#26.3) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.45746641 -0.88778349 -0.05064549 275.77079696  
-0.69608083 0.32207858 0.64166727 143.83899735  
-0.55334978 0.32879458 -0.76530919 246.76254892  
Axis -0.50270755 0.80771908 0.30801786  
Axis point 205.38970331 0.00000000 66.05855727  
Rotation angle (degrees) 161.86918570  
Shift along axis 53.55671210  
  

> fitmap #26.4 inMap #6

Fit molecule COPI_cyto_J4021_model D (#26.4) to map
W20_J4021_consensus_resampled.mrc (#6) using 4745 atoms  
average map value = 0.3102, steps = 84  
shifted from previous position = 1.18  
rotated from previous position = 1.93 degrees  
atoms outside contour = 1692, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model D (#26.4) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.36883139 -0.91668768 -0.15377619 275.04474343  
-0.80433110 0.23185065 0.54708023 165.03207524  
-0.46584859 0.32546733 -0.82283420 243.51890015  
Axis -0.55555262 0.78232196 0.28166228  
Axis point 210.98432459 0.00000000 72.73645940  
Rotation angle (degrees) 168.49504583  
Shift along axis 44.89647919  
  

> fitmap #26.5 inMap #6

Fit molecule COPI_cyto_J4021_model E (#26.5) to map
W20_J4021_consensus_resampled.mrc (#6) using 1876 atoms  
average map value = 0.2655, steps = 44  
shifted from previous position = 0.37  
rotated from previous position = 1.44 degrees  
atoms outside contour = 812, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model E (#26.5) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.37950572 -0.91098051 -0.16152380 276.55156047  
-0.78154710 0.22222838 0.58292255 160.94019650  
-0.49513590 0.34746090 -0.79631111 243.08456807  
Axis -0.54968179 0.77881257 0.30216041  
Axis point 210.99674193 0.00000000 69.29658337  
Rotation angle (degrees) 167.63257816  
Shift along axis 46.77742440  
  

> fitmap #26.6 inMap #6

Fit molecule COPI_cyto_J4021_model F (#26.6) to map
W20_J4021_consensus_resampled.mrc (#6) using 2400 atoms  
average map value = 0.3003, steps = 72  
shifted from previous position = 3.77  
rotated from previous position = 7.24 degrees  
atoms outside contour = 749, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model F (#26.6) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.50121599 -0.84817893 -0.17139150 277.75765218  
-0.73837669 0.31593590 0.59580566 148.29415474  
-0.45120108 0.42517881 -0.78462767 230.60293751  
Axis -0.49366217 0.80955254 0.31768278  
Axis point 195.53368048 0.00000000 69.77740358  
Rotation angle (degrees) 170.04832921  
Shift along axis 56.19204834  
  

> fitmap #26.7 inMap #6

Fit molecule COPI_cyto_J4021_model G (#26.7) to map
W20_J4021_consensus_resampled.mrc (#6) using 2302 atoms  
average map value = 0.3136, steps = 76  
shifted from previous position = 3.03  
rotated from previous position = 3.18 degrees  
atoms outside contour = 723, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model G (#26.7) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.43399059 -0.88593113 -0.16364048 278.30290158  
-0.75953045 0.26210802 0.59532587 156.65606797  
-0.48452624 0.38265575 -0.78664408 237.63722363  
Axis -0.52487405 0.79195238 0.31195938  
Axis point 205.37019802 0.00000000 68.21146617  
Rotation angle (degrees) 168.31145195  
Shift along axis 52.12333508  
  

> fitmap #26.8 inMap #6

Fit molecule COPI_cyto_J4021_model H (#26.8) to map
W20_J4021_consensus_resampled.mrc (#6) using 420 atoms  
average map value = 0.4011, steps = 52  
shifted from previous position = 2.32  
rotated from previous position = 1.55 degrees  
atoms outside contour = 112, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model H (#26.8) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.41519620 -0.89510830 -0.16246005 278.00922432  
-0.77921085 0.25774528 0.57131239 160.68655904  
-0.46951315 0.36379736 -0.80449295 240.32587092  
Axis -0.53442036 0.79076406 0.29847457  
Axis point 207.26688590 0.00000000 70.94580099  
Rotation angle (degrees) 168.80494855  
Shift along axis 50.22252640  
  

> fitmap #26.9 inMap #6

Fit molecule COPI_cyto_J4021_model I (#26.9) to map
W20_J4021_consensus_resampled.mrc (#6) using 1573 atoms  
average map value = 0.2888, steps = 112  
shifted from previous position = 1.44  
rotated from previous position = 3.06 degrees  
atoms outside contour = 702, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model I (#26.9) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.37846625 -0.91010040 -0.16876189 276.33040233  
-0.76836367 0.20723976 0.60553197 162.64450565  
-0.51612071 0.35884392 -0.77772133 243.67694950  
Axis -0.54941463 0.77362488 0.31567087  
Axis point 212.64433272 0.00000000 66.29298345  
Rotation angle (degrees) 167.02647454  
Shift along axis 50.92758584  
  

> fitmap #26.10 inMap #6

Fit molecule COPI_cyto_J4021_model J (#26.10) to map
W20_J4021_consensus_resampled.mrc (#6) using 1112 atoms  
average map value = 0.3374, steps = 68  
shifted from previous position = 0.981  
rotated from previous position = 4.81 degrees  
atoms outside contour = 408, contour level = 0.25941  
  
Position of COPI_cyto_J4021_model J (#26.10) relative to
W20_J4021_consensus_resampled.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.36533925 -0.92641223 -0.09103639 268.10331410  
-0.79596275 0.26018434 0.54657793 163.12428402  
-0.48267023 0.27214795 -0.83244517 250.25943922  
Axis -0.55363524 0.79008238 0.26316888  
Axis point 210.17105433 0.00000000 74.56081239  
Rotation angle (degrees) 165.65005163  
Shift along axis 46.31067629  
  

> hide #!26 models

> split #27 chains

Split COPI_cyto_J4022_model (#27) into 13 models  
Chain information for COPI_cyto_J4022_model A #27.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4022_model B #27.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4022_model C #27.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4022_model D #27.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4022_model E #27.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4022_model F #27.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4022_model G #27.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4022_model H #27.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4022_model I #27.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4022_model J #27.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4022_model K #27.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4022_model L #27.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4022_model M #27.13  
---  
Chain | Description  
M | No description available  
  

> hide #!6 models

> show #!8 models

> color #8 darkgrey models

> color #8 #a9a9a9c0 models

> color #8 #a9a9a9bf models

> hide #!27 models

> show #!27 models

> show #27.1 models

> show #27.2 models

> show #27.3 models

> show #!27.4 models

> show #27.5 models

> show #27.6 models

> show #27.7 models

> show #27.8 models

> show #27.9 models

> show #27.10 models

> show #27.11 models

> show #27.12 models

> show #27.13 models

> fitmap #27.1 inMap #8

Fit molecule COPI_cyto_J4022_model A (#27.1) to map
W20_J4022_consensus_resampled.mrc (#8) using 2590 atoms  
average map value = 0.2646, steps = 56  
shifted from previous position = 1.25  
rotated from previous position = 2.42 degrees  
atoms outside contour = 957, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model A (#27.1) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.39256776 -0.89898632 -0.19420133 280.18889645  
-0.78978108 0.22129853 0.57207763 162.30513777  
-0.47131349 0.37795577 -0.79687705 238.21825154  
Axis -0.54600989 0.77943814 0.30716346  
Axis point 209.81036508 0.00000000 69.55927246  
Rotation angle (degrees) 169.76045090  
Shift along axis 46.69284574  
  

> fitmap #27.2 inMap #8

Fit molecule COPI_cyto_J4022_model B (#27.2) to map
W20_J4022_consensus_resampled.mrc (#8) using 2426 atoms  
average map value = 0.2446, steps = 52  
shifted from previous position = 1.11  
rotated from previous position = 2.79 degrees  
atoms outside contour = 1336, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model B (#27.2) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.38976486 -0.89769297 -0.20550111 280.56757169  
-0.80102851 0.22038063 0.55658397 165.91242827  
-0.45435305 0.38154912 -0.80497428 236.80345949  
Axis -0.54830136 0.77953535 0.30280399  
Axis point 210.09627043 0.00000000 70.38992448  
Rotation angle (degrees) 170.81541733  
Shift along axis 47.20405452  
  

> fitmap #27.3 inMap #8

Fit molecule COPI_cyto_J4022_model C (#27.3) to map
W20_J4022_consensus_resampled.mrc (#8) using 1612 atoms  
average map value = 0.2655, steps = 76  
shifted from previous position = 1.78  
rotated from previous position = 8.48 degrees  
atoms outside contour = 633, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model C (#27.3) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.44384488 -0.89370270 -0.06555325 276.26301732  
-0.70850239 0.30519488 0.63630219 146.54842255  
-0.54865846 0.32886410 -0.76864967 245.76532786  
Axis -0.51083267 0.80271747 0.30772494  
Axis point 206.80155193 0.00000000 65.73198008  
Rotation angle (degrees) 162.48721631  
Shift along axis 52.14092594  
  

> fitmap #27.4 inMap #8

Fit molecule COPI_cyto_J4022_model D (#27.4) to map
W20_J4022_consensus_resampled.mrc (#8) using 4745 atoms  
average map value = 0.3044, steps = 100  
shifted from previous position = 0.615  
rotated from previous position = 1.41 degrees  
atoms outside contour = 1677, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model D (#27.4) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.37672030 -0.91435784 -0.14843034 275.26026826  
-0.79965882 0.24012360 0.55035120 163.64023290  
-0.46757631 0.32602210 -0.82163374 244.18290661  
Axis -0.55170270 0.78489010 0.28208449  
Axis point 210.28195260 0.00000000 73.03172771  
Rotation angle (degrees) 168.26963934  
Shift along axis 45.45797518  
  

> fitmap #27.5 inMap #8

Fit molecule COPI_cyto_J4022_model E (#27.5) to map
W20_J4022_consensus_resampled.mrc (#8) using 1876 atoms  
average map value = 0.2625, steps = 52  
shifted from previous position = 0.552  
rotated from previous position = 1.61 degrees  
atoms outside contour = 794, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model E (#27.5) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.39012142 -0.90485684 -0.17040949 278.02588034  
-0.78445694 0.22972243 0.57606852 161.46943730  
-0.48211265 0.35841557 -0.79944086 241.20120653  
Axis -0.54579308 0.78163622 0.30191841  
Axis point 210.00611855 0.00000000 69.84237754  
Rotation angle (degrees) 168.49862507  
Shift along axis 47.28884646  
  

> fitmap #27.6 inMap #8

Fit molecule COPI_cyto_J4022_model F (#27.6) to map
W20_J4022_consensus_resampled.mrc (#8) using 2400 atoms  
average map value = 0.2992, steps = 68  
shifted from previous position = 0.833  
rotated from previous position = 1.23 degrees  
atoms outside contour = 836, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model F (#27.6) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.37627915 -0.91501112 -0.14549456 274.06344417  
-0.78910526 0.23420927 0.56785467 161.94404988  
-0.48551716 0.32848239 -0.81016814 243.51929054  
Axis -0.55094864 0.78260937 0.28978988  
Axis point 210.19577001 0.00000000 70.73622595  
Rotation angle (degrees) 167.45323080  
Shift along axis 46.31347447  
  

> fitmap #27.7 inMap #8

Fit molecule COPI_cyto_J4022_model G (#27.7) to map
W20_J4022_consensus_resampled.mrc (#8) using 2302 atoms  
average map value = 0.2826, steps = 96  
shifted from previous position = 2.92  
rotated from previous position = 2.79 degrees  
atoms outside contour = 976, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model G (#27.7) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.33451130 -0.92639130 -0.17292012 274.85479282  
-0.79442923 0.17849847 0.58053467 167.37506321  
-0.50693629 0.33156820 -0.79566208 241.26568780  
Axis -0.56972315 0.76434688 0.30197578  
Axis point 216.29332055 0.00000000 65.86543953  
Rotation angle (degrees) 167.37918527  
Shift along axis 44.19786245  
  

> fitmap #27.8 inMap #8

Fit molecule COPI_cyto_J4022_model H (#27.8) to map
W20_J4022_consensus_resampled.mrc (#8) using 420 atoms  
average map value = 0.3956, steps = 60  
shifted from previous position = 3.43  
rotated from previous position = 4.58 degrees  
atoms outside contour = 107, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model H (#27.8) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.29409810 -0.94159516 -0.16402708 273.35842395  
-0.82182141 0.16150890 0.54637392 173.87777684  
-0.48797119 0.29548850 -0.82132252 245.93686122  
Axis -0.58771482 0.75885938 0.28057750  
Axis point 220.70161074 0.00000000 69.69363620  
Rotation angle (degrees) 167.67589275  
Shift along axis 40.29633569  
  

> fitmap #27.9 inMap #8

Fit molecule COPI_cyto_J4022_model I (#27.9) to map
W20_J4022_consensus_resampled.mrc (#8) using 1573 atoms  
average map value = 0.2808, steps = 104  
shifted from previous position = 1.41  
rotated from previous position = 3.01 degrees  
atoms outside contour = 658, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model I (#27.9) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.32433234 -0.92767253 -0.18501954 273.90297834  
-0.82148476 0.17924210 0.54132715 171.93921965  
-0.46901103 0.32756063 -0.82020284 242.13807924  
Axis -0.57622748 0.76552540 0.28623898  
Axis point 215.70475315 0.00000000 70.66930942  
Rotation angle (degrees) 169.31041717  
Shift along axis 43.10277500  
  

> fitmap #27.10 inMap #8

Fit molecule COPI_cyto_J4022_model J (#27.10) to map
W20_J4022_consensus_resampled.mrc (#8) using 1112 atoms  
average map value = 0.33, steps = 88  
shifted from previous position = 0.662  
rotated from previous position = 3.39 degrees  
atoms outside contour = 391, contour level = 0.25565  
  
Position of COPI_cyto_J4022_model J (#27.10) relative to
W20_J4022_consensus_resampled.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.38171857 -0.91794952 -0.10797977 270.82825471  
-0.78627841 0.26109129 0.55999787 160.73450027  
-0.48585720 0.29866375 -0.82142727 248.07112012  
Axis -0.54679573 0.79064209 0.27549866  
Axis point 209.01509765 0.00000000 73.28198391  
Rotation angle (degrees) 166.17432003  
Shift along axis 47.33898908  
  

> hide #!27 models

> show #!28 models

> split #28 chains

Split COPI_cyto_J4023_model (#28) into 13 models  
Chain information for COPI_cyto_J4023_model A #28.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4023_model B #28.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4023_model C #28.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4023_model D #28.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4023_model E #28.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4023_model F #28.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4023_model G #28.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4023_model H #28.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4023_model I #28.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4023_model J #28.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4023_model K #28.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4023_model L #28.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4023_model M #28.13  
---  
Chain | Description  
M | No description available  
  

> hide #!8 models

> show #!10 models

> color #10 darkgrey models

> color #10 #a9a9a9c3 models

> color #10 #a9a9a9c1 models

> color #10 #a9a9a9c0 models

> color #10 #a9a9a9bf models

> fitmap #28.1 inMap #10

Fit molecule COPI_cyto_J4023_model A (#28.1) to map
W20_J4023_consensus_resampled.mrc (#10) using 2590 atoms  
average map value = 0.2661, steps = 80  
shifted from previous position = 0.302  
rotated from previous position = 1.64 degrees  
atoms outside contour = 989, contour level = 0.259  
  
Position of COPI_cyto_J4023_model A (#28.1) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.38904601 -0.90521909 -0.17094331 278.16947599  
-0.78384179 0.22779200 0.57767021 160.52070200  
-0.48397858 0.35873280 -0.79817011 240.89357120  
Axis -0.54622301 0.78098606 0.30282204  
Axis point 209.92132129 0.00000000 69.65657344  
Rotation angle (degrees) 168.43904812  
Shift along axis 46.36974623  
  

> fitmap #28.2 inMap #10

Fit molecule COPI_cyto_J4023_model B (#28.2) to map
W20_J4023_consensus_resampled.mrc (#10) using 2426 atoms  
average map value = 0.2462, steps = 52  
shifted from previous position = 0.807  
rotated from previous position = 1.71 degrees  
atoms outside contour = 1372, contour level = 0.259  
  
Position of COPI_cyto_J4023_model B (#28.2) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.37936173 -0.90522783 -0.19143475 278.45387337  
-0.80078335 0.21757935 0.55803698 165.73257662  
-0.46349835 0.36499563 -0.80743265 238.99424212  
Axis -0.55224090 0.77830294 0.29878840  
Axis point 210.75764690 0.00000000 70.47418382  
Rotation angle (degrees) 169.93414364  
Shift along axis 46.62524128  
  

> fitmap #28.3 inMap #10

Fit molecule COPI_cyto_J4023_model C (#28.3) to map
W20_J4023_consensus_resampled.mrc (#10) using 1612 atoms  
average map value = 0.2674, steps = 100  
shifted from previous position = 1.78  
rotated from previous position = 13.1 degrees  
atoms outside contour = 645, contour level = 0.259  
  
Position of COPI_cyto_J4023_model C (#28.3) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.48320445 -0.87548576 -0.00617812 274.93344286  
-0.65530471 0.35698291 0.66568683 136.56063023  
-0.58059385 0.32571139 -0.74620566 247.99422947  
Axis -0.48370086 0.81725132 0.31326310  
Axis point 203.45931463 0.00000000 64.26982521  
Rotation angle (degrees) 159.42510249  
Shift along axis 56.30625377  
  

> fitmap #28.4 inMap #10

Fit molecule COPI_cyto_J4023_model D (#28.4) to map
W20_J4023_consensus_resampled.mrc (#10) using 4745 atoms  
average map value = 0.2995, steps = 72  
shifted from previous position = 0.314  
rotated from previous position = 1.26 degrees  
atoms outside contour = 1741, contour level = 0.259  
  
Position of COPI_cyto_J4023_model D (#28.4) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.37631952 -0.91385434 -0.15249221 275.60221900  
-0.80067150 0.23796533 0.54981604 164.18546643  
-0.46616391 0.32900267 -0.82124812 243.17403703  
Axis -0.55210445 0.78428015 0.28299352  
Axis point 210.42278812 0.00000000 72.60304045  
Rotation angle (degrees) 168.46454551  
Shift along axis 45.42286901  
  

> fitmap #28.5 inMap #10

Fit molecule COPI_cyto_J4023_model E (#28.5) to map
W20_J4023_consensus_resampled.mrc (#10) using 1876 atoms  
average map value = 0.2617, steps = 64  
shifted from previous position = 0.422  
rotated from previous position = 1.48 degrees  
atoms outside contour = 839, contour level = 0.259  
  
Position of COPI_cyto_J4023_model E (#28.5) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.38829706 -0.90758205 -0.15975054 277.05830941  
-0.78302109 0.23353287 0.57648971 160.99119705  
-0.48590471 0.34893730 -0.80133600 242.27299446  
Axis -0.54602993 0.78263260 0.29889383  
Axis point 210.04637843 0.00000000 70.01691196  
Rotation angle (degrees) 167.97315842  
Shift along axis 47.12873327  
  

> fitmap #28.6 inMap #10

Fit molecule COPI_cyto_J4023_model F (#28.6) to map
W20_J4023_consensus_resampled.mrc (#10) using 2400 atoms  
average map value = 0.3111, steps = 56  
shifted from previous position = 2.06  
rotated from previous position = 4.34 degrees  
atoms outside contour = 741, contour level = 0.259  
  
Position of COPI_cyto_J4023_model F (#28.6) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.35666068 -0.90337062 -0.23814849 281.82055176  
-0.82036020 0.18087540 0.54248801 172.36641935  
-0.44699252 0.38885168 -0.80560044 235.22166541  
Axis -0.56435649 0.76715244 0.30492440  
Axis point 214.18344574 0.00000000 69.66627251  
Rotation angle (degrees) 172.17681998  
Shift along axis 44.90888683  
  

> fitmap #28.7 inMap #10

Fit molecule COPI_cyto_J4023_model G (#28.7) to map
W20_J4023_consensus_resampled.mrc (#10) using 2302 atoms  
average map value = 0.2755, steps = 64  
shifted from previous position = 1.24  
rotated from previous position = 2.83 degrees  
atoms outside contour = 963, contour level = 0.259  
  
Position of COPI_cyto_J4023_model G (#28.7) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.37482050 -0.90249978 -0.21214088 278.18486892  
-0.80142293 0.20037819 0.56353340 166.38017125  
-0.46608036 0.38123844 -0.79838986 235.86468916  
Axis -0.55487743 0.77295215 0.30766217  
Axis point 210.65854364 0.00000000 68.54942126  
Rotation angle (degrees) 170.54540398  
Shift along axis 46.81204878  
  

> fitmap #28.8 inMap #10

Fit molecule COPI_cyto_J4023_model H (#28.8) to map
W20_J4023_consensus_resampled.mrc (#10) using 420 atoms  
average map value = 0.3956, steps = 56  
shifted from previous position = 0.904  
rotated from previous position = 5.89 degrees  
atoms outside contour = 91, contour level = 0.259  
  
Position of COPI_cyto_J4023_model H (#28.8) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.28058215 -0.93606717 -0.21225441 275.82091929  
-0.83301532 0.12762624 0.53832800 180.46362086  
-0.47682192 0.32785640 -0.81556793 244.72635677  
Axis -0.59550860 0.74856765 0.29157501  
Axis point 223.51865643 0.00000000 69.31481173  
Rotation angle (degrees) 169.82147556  
Shift along axis 42.19158968  
  

> fitmap #28.9 inMap #10

Fit molecule COPI_cyto_J4023_model I (#28.9) to map
W20_J4023_consensus_resampled.mrc (#10) using 1573 atoms  
average map value = 0.285, steps = 68  
shifted from previous position = 1.1  
rotated from previous position = 2.83 degrees  
atoms outside contour = 662, contour level = 0.259  
  
Position of COPI_cyto_J4023_model I (#28.9) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.34800803 -0.91546944 -0.20200525 275.41256013  
-0.79922182 0.17708111 0.57435771 168.85645411  
-0.49003561 0.36132810 -0.79328880 241.32530949  
Axis -0.56560752 0.76473942 0.30864502  
Axis point 214.22374441 0.00000000 67.79866361  
Rotation angle (degrees) 169.14528401  
Shift along axis 47.83962632  
  

> fitmap #28.10 inMap #10

Fit molecule COPI_cyto_J4023_model J (#28.10) to map
W20_J4023_consensus_resampled.mrc (#10) using 1112 atoms  
average map value = 0.3207, steps = 84  
shifted from previous position = 0.351  
rotated from previous position = 3.94 degrees  
atoms outside contour = 429, contour level = 0.259  
  
Position of COPI_cyto_J4023_model J (#28.10) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.37572939 -0.92009445 -0.11069619 271.04311764  
-0.80434258 0.26444766 0.53207186 165.17448016  
-0.46028301 0.28895269 -0.83943190 247.79248250  
Axis -0.55095733 0.79223463 0.26231720  
Axis point 209.56379921 0.00000000 75.63736830  
Rotation angle (degrees) 167.25376251  
Shift along axis 46.52397993  
  

> hide #!10 models

> show #!12 models

> color #12 darkgrey models

> color #12 #a9a9a9c0 models

> color #12 #a9a9a9bf models

> hide #!28 models

> show #!29 models

> split #29 chains

Split COPI_cyto_J4024_model (#29) into 13 models  
Chain information for COPI_cyto_J4024_model A #29.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4024_model B #29.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4024_model C #29.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4024_model D #29.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4024_model E #29.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4024_model F #29.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4024_model G #29.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4024_model H #29.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4024_model I #29.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4024_model J #29.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4024_model K #29.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4024_model L #29.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4024_model M #29.13  
---  
Chain | Description  
M | No description available  
  

> fitmap #29.1 inMap #12

Fit molecule COPI_cyto_J4024_model A (#29.1) to map
W20_J4024_consensus_resampled.mrc (#12) using 2590 atoms  
average map value = 0.2692, steps = 100  
shifted from previous position = 0.874  
rotated from previous position = 1.25 degrees  
atoms outside contour = 892, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model A (#29.1) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.38195228 -0.90644822 -0.18017798 277.95847443  
-0.79414648 0.22219499 0.56565075 163.75119780  
-0.47269847 0.35913930 -0.80472054 240.33850306  
Axis -0.55030232 0.77949527 0.29925655  
Axis point 210.52708604 0.00000000 70.30220517  
Rotation angle (degrees) 169.18522876  
Shift along axis 46.60496312  
  

> fitmap #29.2 inMap #12

Fit molecule COPI_cyto_J4024_model B (#29.2) to map
W20_J4024_consensus_resampled.mrc (#12) using 2426 atoms  
average map value = 0.2485, steps = 64  
shifted from previous position = 0.888  
rotated from previous position = 2.24 degrees  
atoms outside contour = 1271, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model B (#29.2) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.37729450 -0.90386908 -0.20166693 279.03898781  
-0.80059309 0.20887819 0.56162321 165.93012621  
-0.46551002 0.37335050 -0.80243993 238.54192108  
Axis -0.55344239 0.77558746 0.30358789  
Axis point 211.11340356 0.00000000 69.95800816  
Rotation angle (degrees) 170.20680766  
Shift along axis 46.67975878  
  

> fitmap #29.3 inMap #12

Fit molecule COPI_cyto_J4024_model C (#29.3) to map
W20_J4024_consensus_resampled.mrc (#12) using 1612 atoms  
average map value = 0.2695, steps = 160  
shifted from previous position = 2.41  
rotated from previous position = 18.3 degrees  
atoms outside contour = 621, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model C (#29.3) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.48164802 -0.86999176 0.10549661 268.61459966  
-0.62073770 0.42365137 0.65970011 129.62131912  
-0.61862744 0.25225752 -0.74408753 255.46187775  
Axis -0.46969429 0.83476038 0.28733670  
Axis point 203.50844953 0.00000000 65.15506927  
Rotation angle (degrees) 154.29538375  
Shift along axis 55.43957254  
  

> fitmap #29.4 inMap #12

Fit molecule COPI_cyto_J4024_model D (#29.4) to map
W20_J4024_consensus_resampled.mrc (#12) using 4745 atoms  
average map value = 0.311, steps = 96  
shifted from previous position = 0.393  
rotated from previous position = 1.84 degrees  
atoms outside contour = 1582, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model D (#29.4) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.36490275 -0.91923092 -0.14785303 274.26364105  
-0.80817834 0.23388135 0.54050653 165.94975145  
-0.46227025 0.31672393 -0.82824645 244.92475483  
Axis -0.55725013 0.78294306 0.27653654  
Axis point 211.24999279 0.00000000 73.77234724  
Rotation angle (degrees) 168.41673025  
Shift along axis 44.82640132  
  

> fitmap #29.5 inMap #12

Fit molecule COPI_cyto_J4024_model E (#29.5) to map
W20_J4024_consensus_resampled.mrc (#12) using 1876 atoms  
average map value = 0.2646, steps = 56  
shifted from previous position = 0.686  
rotated from previous position = 1.54 degrees  
atoms outside contour = 791, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model E (#29.5) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.38725918 -0.90565201 -0.17269853 278.00845664  
-0.78536225 0.22592118 0.57633824 161.81751759  
-0.48294563 0.35882318 -0.79875495 241.37260249  
Axis -0.54715674 0.78042314 0.30258755  
Axis point 210.33473059 0.00000000 69.77477808  
Rotation angle (degrees) 168.53504549  
Shift along axis 47.20827915  
  

> fitmap #29.6 inMap #12

Fit molecule COPI_cyto_J4024_model F (#29.6) to map
W20_J4024_consensus_resampled.mrc (#12) using 2400 atoms  
average map value = 0.242, steps = 84  
shifted from previous position = 5.87  
rotated from previous position = 13.7 degrees  
atoms outside contour = 1297, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model F (#29.6) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.53159589 -0.84531226 -0.05341354 266.88246547  
-0.64371973 0.36222400 0.67410585 127.52327824  
-0.55048227 0.39273525 -0.73670097 230.79457007  
Axis -0.46452916 0.82063626 0.33281944  
Axis point 189.53211141 0.00000000 61.79948623  
Rotation angle (degrees) 162.37079623  
Shift along axis 57.48845832  
  

> fitmap #29.7 inMap #12

Fit molecule COPI_cyto_J4024_model G (#29.7) to map
W20_J4024_consensus_resampled.mrc (#12) using 2302 atoms  
average map value = 0.2775, steps = 60  
shifted from previous position = 3.1  
rotated from previous position = 4.14 degrees  
atoms outside contour = 948, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model G (#29.7) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.36698963 -0.92232957 -0.12094124 274.70465819  
-0.76065109 0.22270273 0.60976506 158.64044193  
-0.53547040 0.31577154 -0.78330058 243.71016364  
Axis -0.55127458 0.77729395 0.30316736  
Axis point 213.68280008 0.00000000 64.72109245  
Rotation angle (degrees) 164.53504616  
Shift along axis 45.75752709  
  

> fitmap #29.8 inMap #12

Fit molecule COPI_cyto_J4024_model H (#29.8) to map
W20_J4024_consensus_resampled.mrc (#12) using 420 atoms  
average map value = 0.3642, steps = 52  
shifted from previous position = 3.12  
rotated from previous position = 7.89 degrees  
atoms outside contour = 112, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model H (#29.8) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.31100107 -0.94914560 -0.04899985 269.58279474  
-0.77806832 0.22466013 0.58663236 161.32624746  
-0.54579120 0.22056852 -0.80836966 258.53074932  
Axis -0.57164561 0.77578980 0.26715442  
Axis point 220.48916877 0.00000000 70.49015049  
Rotation angle (degrees) 161.32593230  
Shift along axis 40.11707004  
  

> fitmap #29.9 inMap #12

Fit molecule COPI_cyto_J4024_model I (#29.9) to map
W20_J4024_consensus_resampled.mrc (#12) using 1573 atoms  
average map value = 0.308, steps = 88  
shifted from previous position = 1.06  
rotated from previous position = 3.68 degrees  
atoms outside contour = 615, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model I (#29.9) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.32207758 -0.93636157 -0.13961755 272.41905490  
-0.79316925 0.18637492 0.57978181 166.78930021  
-0.51686418 0.29747507 -0.80272038 248.24026118  
Axis -0.57325903 0.76604633 0.29076985  
Axis point 217.83744421 0.00000000 68.18432836  
Rotation angle (degrees) 165.74548655  
Shift along axis 43.78243158  
  

> fitmap #29.10 inMap #12

Fit molecule COPI_cyto_J4024_model J (#29.10) to map
W20_J4024_consensus_resampled.mrc (#12) using 1112 atoms  
average map value = 0.3363, steps = 72  
shifted from previous position = 0.618  
rotated from previous position = 4.66 degrees  
atoms outside contour = 406, contour level = 0.25569  
  
Position of COPI_cyto_J4024_model J (#29.10) relative to
W20_J4024_consensus_resampled.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.36498462 -0.92690394 -0.08738035 267.73871712  
-0.79378094 0.26076630 0.54946590 162.75689323  
-0.48651625 0.26990746 -0.83093436 251.13764208  
Axis -0.55340845 0.79012166 0.26352770  
Axis point 210.27082462 0.00000000 74.58174748  
Rotation angle (degrees) 165.36983736  
Shift along axis 46.61060410  
  

> hide #!12 models

> hide #!29 models

> show #!30 models

> split #30 chains

Split COPI_cyto_J4025_model (#30) into 13 models  
Chain information for COPI_cyto_J4025_model A #30.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4025_model B #30.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4025_model C #30.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4025_model D #30.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4025_model E #30.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4025_model F #30.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4025_model G #30.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4025_model H #30.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4025_model I #30.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4025_model J #30.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4025_model K #30.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4025_model L #30.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4025_model M #30.13  
---  
Chain | Description  
M | No description available  
  

> show #!14 models

> color #14 darkgrey models

> color #14 #a9a9a9be models

> color #14 #a9a9a9bf models

> fitmap #30.1 inMap #14

Fit molecule COPI_cyto_J4025_model A (#30.1) to map
W20_J4025_consensus_resampled.mrc (#14) using 2590 atoms  
average map value = 0.2675, steps = 76  
shifted from previous position = 0.303  
rotated from previous position = 0.916 degrees  
atoms outside contour = 971, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model A (#30.1) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.38101620 -0.91006695 -0.16310984 276.49091025  
-0.78874603 0.22789915 0.57091304 162.02364661  
-0.48239649 0.34617935 -0.80464495 242.12831797  
Axis -0.54965686 0.78091585 0.29672844  
Axis point 210.37135033 0.00000000 70.30651243  
Rotation angle (degrees) 168.20381385  
Shift along axis 46.39806523  
  

> fitmap #30.2 inMap #14

Fit molecule COPI_cyto_J4025_model B (#30.2) to map
W20_J4025_consensus_resampled.mrc (#14) using 2426 atoms  
average map value = 0.2464, steps = 56  
shifted from previous position = 0.713  
rotated from previous position = 1.44 degrees  
atoms outside contour = 1409, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model B (#30.2) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.37124088 -0.90903393 -0.18930807 277.53484582  
-0.80004519 0.20967074 0.56210843 165.71657123  
-0.47128327 0.36013264 -0.80510656 240.05521807  
Axis -0.55553559 0.77557441 0.29977415  
Axis point 211.48229973 0.00000000 70.08195116  
Rotation angle (degrees) 169.52626651  
Shift along axis 46.30739501  
  

> fitmap #30.3 inMap #14

Fit molecule COPI_cyto_J4025_model C (#30.3) to map
W20_J4025_consensus_resampled.mrc (#14) using 1612 atoms  
average map value = 0.2632, steps = 96  
shifted from previous position = 1.92  
rotated from previous position = 10.7 degrees  
atoms outside contour = 694, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model C (#30.3) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.44316515 -0.89625169 -0.01837289 273.18677871  
-0.69089200 0.32841899 0.64405685 142.84601321  
-0.57120303 0.29811723 -0.76475697 249.76514069  
Axis -0.50596953 0.80856656 0.30035804  
Axis point 206.79517933 0.00000000 65.69504944  
Rotation angle (degrees) 160.00987675  
Shift along axis 52.29529270  
  

> fitmap #30.4 inMap #14

Fit molecule COPI_cyto_J4025_model D (#30.4) to map
W20_J4025_consensus_resampled.mrc (#14) using 4745 atoms  
average map value = 0.2994, steps = 96  
shifted from previous position = 0.519  
rotated from previous position = 1.3 degrees  
atoms outside contour = 1727, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model D (#30.4) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.37140408 -0.91616900 -0.15064322 274.98034054  
-0.80234855 0.23505413 0.54862225 164.28861064  
-0.46722138 0.32462891 -0.82238693 243.65233050  
Axis -0.55421176 0.78328822 0.28161834  
Axis point 210.66577055 0.00000000 72.75003830  
Rotation angle (degrees) 168.34121758  
Shift along axis 44.90495816  
  

> fitmap #30.5 inMap #14

Fit molecule COPI_cyto_J4025_model E (#30.5) to map
W20_J4025_consensus_resampled.mrc (#14) using 1876 atoms  
average map value = 0.2637, steps = 64  
shifted from previous position = 0.305  
rotated from previous position = 1.58 degrees  
atoms outside contour = 846, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model E (#30.5) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.38354345 -0.90936875 -0.16106801 276.77746085  
-0.78111798 0.22638522 0.58189729 160.60505785  
-0.49269579 0.34899601 -0.79715284 242.75004629  
Axis -0.54793741 0.78020725 0.30173041  
Axis point 210.53234092 0.00000000 69.48347841  
Rotation angle (degrees) 167.72960946  
Shift along axis 46.89357823  
  

> fitmap #30.6 inMap #14

Fit molecule COPI_cyto_J4025_model F (#30.6) to map
W20_J4025_consensus_resampled.mrc (#14) using 2400 atoms  
average map value = 0.3154, steps = 76  
shifted from previous position = 4.38  
rotated from previous position = 6.32 degrees  
atoms outside contour = 716, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model F (#30.6) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.46916307 -0.86826583 -0.16124662 276.76831771  
-0.75844576 0.30262715 0.57721474 152.99334716  
-0.45237823 0.39310465 -0.80051401 236.07204224  
Axis -0.50923185 0.80524369 0.30375239  
Axis point 199.19186600 0.00000000 71.96275109  
Rotation angle (degrees) 169.58524914  
Shift along axis 53.96513192  
  

> fitmap #30.7 inMap #14

Fit molecule COPI_cyto_J4025_model G (#30.7) to map
W20_J4025_consensus_resampled.mrc (#14) using 2302 atoms  
average map value = 0.2919, steps = 76  
shifted from previous position = 4.85  
rotated from previous position = 4.34 degrees  
atoms outside contour = 830, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model G (#30.7) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.43043084 -0.88252203 -0.18943119 279.00638393  
-0.77202835 0.25122185 0.58383201 159.76771478  
-0.46765535 0.39754556 -0.78946565 235.51132473  
Axis -0.52833633 0.78908543 0.31337663  
Axis point 205.32244175 0.00000000 68.76349381  
Rotation angle (degrees) 169.84595276  
Shift along axis 52.46491169  
  

> fitmap #30.8 inMap #14

Fit molecule COPI_cyto_J4025_model H (#30.8) to map
W20_J4025_consensus_resampled.mrc (#14) using 420 atoms  
average map value = 0.3536, steps = 80  
shifted from previous position = 3.69  
rotated from previous position = 5.02 degrees  
atoms outside contour = 122, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model H (#30.8) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.35116806 -0.91592354 -0.19433237 278.04382885  
-0.84420748 0.21996160 0.48880532 174.65406664  
-0.40496263 0.33570965 -0.85047299 242.78401221  
Axis -0.56683990 0.77986296 0.26553022  
Axis point 212.55649174 0.00000000 78.50487362  
Rotation angle (degrees) 172.23888649  
Shift along axis 43.06639339  
  

> fitmap #30.9 inMap #14

Fit molecule COPI_cyto_J4025_model I (#30.9) to map
W20_J4025_consensus_resampled.mrc (#14) using 1573 atoms  
average map value = 0.2801, steps = 68  
shifted from previous position = 1.75  
rotated from previous position = 3.58 degrees  
atoms outside contour = 701, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model I (#30.9) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.38742239 -0.89858889 -0.20601436 277.54357463  
-0.78023576 0.20056569 0.59245724 165.02578227  
-0.49105608 0.39027097 -0.77881481 238.87427461  
Axis -0.54798153 0.77254303 0.32077019  
Axis point 210.67928153 0.00000000 66.74726373  
Rotation angle (degrees) 169.36902321  
Shift along axis 52.02451216  
  

> fitmap #30.10 inMap #14

Fit molecule COPI_cyto_J4025_model J (#30.10) to map
W20_J4025_consensus_resampled.mrc (#14) using 1112 atoms  
average map value = 0.3297, steps = 72  
shifted from previous position = 0.309  
rotated from previous position = 4.19 degrees  
atoms outside contour = 404, contour level = 0.25978  
  
Position of COPI_cyto_J4025_model J (#30.10) relative to
W20_J4025_consensus_resampled.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.35980949 -0.92767682 -0.09976404 268.82850280  
-0.80210592 0.25292807 0.54097459 164.87500239  
-0.47661645 0.27466912 -0.83510098 249.92805127  
Axis -0.55685591 0.78801420 0.26257402  
Axis point 210.98119167 0.00000000 74.83620925  
Rotation angle (degrees) 166.16567308  
Shift along axis 45.84971671  
  

> hide #!30 models

> split #31 chains

Split COPI_cyto_J4026_model (#31) into 13 models  
Chain information for COPI_cyto_J4026_model A #31.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4026_model B #31.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4026_model C #31.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4026_model D #31.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4026_model E #31.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4026_model F #31.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4026_model G #31.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4026_model H #31.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4026_model I #31.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4026_model J #31.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4026_model K #31.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4026_model L #31.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4026_model M #31.13  
---  
Chain | Description  
M | No description available  
  

> show #31.1 models

> show #31.2 models

> show #31.3 models

> show #!31.4 models

> show #31.5 models

> show #31.6 models

> show #31.7 models

> show #31.8 models

> show #31.9 models

> show #31.10 models

> show #31.11 models

> show #31.12 models

> show #31.13 models

> hide #!14 models

> color #16 darkgrey models

> color #16 #a9a9a9bf models

> show #!16 models

> fitmap #31.1 inMap #16

Fit molecule COPI_cyto_J4026_model A (#31.1) to map
W20_J4026_consensus_resampled.mrc (#16) using 2590 atoms  
average map value = 0.3888, steps = 44  
shifted from previous position = 1.29  
rotated from previous position = 3.47 degrees  
atoms outside contour = 601, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model A (#31.1) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.42179573 -0.88868235 -0.17981118 281.30883739  
-0.78142467 0.25572018 0.56919478 159.93267883  
-0.45985201 0.38059282 -0.80229998 237.51658930  
Axis -0.53238793 0.79050266 0.30276829  
Axis point 207.09091155 0.00000000 70.78659039  
Rotation angle (degrees) 169.79746249  
Shift along axis 48.57427120  
  

> fitmap #31.2 inMap #16

Fit molecule COPI_cyto_J4026_model B (#31.2) to map
W20_J4026_consensus_resampled.mrc (#16) using 2426 atoms  
average map value = 0.3729, steps = 96  
shifted from previous position = 1.87  
rotated from previous position = 3.62 degrees  
atoms outside contour = 599, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model B (#31.2) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.41831806 -0.88734205 -0.19399514 282.19270881  
-0.78598077 0.24658443 0.56694830 161.68081011  
-0.45524088 0.38964115 -0.80058449 236.37167847  
Axis -0.53469530 0.78782425 0.30566958  
Axis point 207.69640372 0.00000000 70.48893010  
Rotation angle (degrees) 170.45617020  
Shift along axis 48.74057955  
  

> fitmap #31.3 inMap #16

Fit molecule COPI_cyto_J4026_model C (#31.3) to map
W20_J4026_consensus_resampled.mrc (#16) using 1612 atoms  
average map value = 0.3193, steps = 132  
shifted from previous position = 1.47  
rotated from previous position = 4.65 degrees  
atoms outside contour = 561, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model C (#31.3) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.38059936 -0.91824851 -0.10937920 274.00313195  
-0.75305941 0.23911656 0.61296396 156.01911017  
-0.53669887 0.31566272 -0.78250328 246.73459431  
Axis -0.54436027 0.78242476 0.30246220  
Axis point 211.94174234 0.00000000 66.53857749  
Rotation angle (degrees) 164.15273201  
Shift along axis 47.54468445  
  

> fitmap #31.4 inMap #16

Fit molecule COPI_cyto_J4026_model D (#31.4) to map
W20_J4026_consensus_resampled.mrc (#16) using 4745 atoms  
average map value = 0.2725, steps = 48  
shifted from previous position = 0.247  
rotated from previous position = 2.27 degrees  
atoms outside contour = 1838, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model D (#31.4) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.36032627 -0.92283158 -0.13618688 272.90164046  
-0.80657650 0.23487967 0.54246282 165.85713835  
-0.46861429 0.30530874 -0.82896757 246.32646884  
Axis -0.55856608 0.78296216 0.27381417  
Axis point 211.65908561 0.00000000 73.73169378  
Rotation angle (degrees) 167.74351385  
Shift along axis 44.87394129  
  

> fitmap #31.5 inMap #16

Fit molecule COPI_cyto_J4026_model E (#31.5) to map
W20_J4026_consensus_resampled.mrc (#16) using 1876 atoms  
average map value = 0.3337, steps = 68  
shifted from previous position = 0.775  
rotated from previous position = 3.95 degrees  
atoms outside contour = 584, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model E (#31.5) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.41217203 -0.89272092 -0.18210871 281.24771125  
-0.76396069 0.22971791 0.60298736 156.90992899  
-0.49646580 0.38765842 -0.77668699 239.04221312  
Axis -0.53537564 0.78159084 0.32013853  
Axis point 208.88799304 0.00000000 67.41763702  
Rotation angle (degrees) 168.39866163  
Shift along axis 48.59281177  
  

> fitmap #31.10 inMap #16

Fit molecule COPI_cyto_J4026_model J (#31.10) to map
W20_J4026_consensus_resampled.mrc (#16) using 1112 atoms  
average map value = 0.275, steps = 132  
shifted from previous position = 1.13  
rotated from previous position = 6.46 degrees  
atoms outside contour = 480, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model J (#31.10) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.39165506 -0.91840010 -0.05610338 267.15064982  
-0.77630145 0.29709402 0.55595973 158.01112550  
-0.49392549 0.26129757 -0.82931369 252.31232484  
Axis -0.53914103 0.80107967 0.25999678  
Axis point 207.59429240 0.00000000 75.03244785  
Rotation angle (degrees) 164.14105481  
Shift along axis 48.14801546  
  

> fitmap #31.10 inMap #16

Fit molecule COPI_cyto_J4026_model J (#31.10) to map
W20_J4026_consensus_resampled.mrc (#16) using 1112 atoms  
average map value = 0.275, steps = 48  
shifted from previous position = 0.0181  
rotated from previous position = 0.0479 degrees  
atoms outside contour = 481, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model J (#31.10) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.39111474 -0.91864714 -0.05582756 267.08423778  
-0.77617700 0.29664639 0.55637235 158.00648729  
-0.49454882 0.26093749 -0.82905555 252.36987731  
Axis -0.53933760 0.80091724 0.26008948  
Axis point 207.64765628 0.00000000 74.98798493  
Rotation angle (degrees) 164.10431634  
Shift along axis 48.14029770  
  

> fitmap #31.12 inMap #16

Fit molecule COPI_cyto_J4026_model L (#31.12) to map
W20_J4026_consensus_resampled.mrc (#16) using 1420 atoms  
average map value = 0.246, steps = 148  
shifted from previous position = 18  
rotated from previous position = 21.2 degrees  
atoms outside contour = 781, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model L (#31.12) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.20471014 -0.86077408 -0.46600619 296.00976398  
-0.82456258 -0.10488916 0.55596297 187.90289621  
-0.52743751 0.49806252 -0.68829022 207.63206185  
Axis -0.63033876 0.66877783 0.39421981  
Axis point 239.98122179 0.00000000 43.12371251  
Rotation angle (degrees) 177.36759071  
Shift along axis 20.93153367  
  

> fitmap #31.13 inMap #16

Fit molecule COPI_cyto_J4026_model M (#31.13) to map
W20_J4026_consensus_resampled.mrc (#16) using 4552 atoms  
average map value = 0.2784, steps = 240  
shifted from previous position = 13.3  
rotated from previous position = 28.4 degrees  
atoms outside contour = 2174, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model M (#31.13) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.19059508 -0.97763486 0.08890226 232.38163718  
-0.95481798 0.20565637 0.21454160 224.73228555  
-0.22802666 -0.04399490 -0.97266043 250.13777446  
Axis -0.63112960 0.77367498 0.05569971  
Axis point 224.43338633 0.00000000 99.69760848  
Rotation angle (degrees) 168.18101146  
Shift along axis 41.13941809  
  

> hide #!31 models

> show #!32 models

> split #32 chains

Split COPI_cyto_J4027_model (#32) into 13 models  
Chain information for COPI_cyto_J4027_model A #32.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4027_model B #32.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4027_model C #32.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4027_model D #32.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4027_model E #32.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4027_model F #32.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4027_model G #32.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4027_model H #32.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4027_model I #32.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4027_model J #32.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4027_model K #32.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4027_model L #32.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4027_model M #32.13  
---  
Chain | Description  
M | No description available  
  

> hide #!16 models

> show #!18 models

> color #18 darkgrey models

> color #18 #a9a9a9be models

> color #18 #a9a9a9bf models

> fitmap #32.1 inMap #18

Fit molecule COPI_cyto_J4027_model A (#32.1) to map
W20_J4027_consensus_resampled.mrc (#18) using 2590 atoms  
average map value = 0.3669, steps = 68  
shifted from previous position = 0.35  
rotated from previous position = 0.41 degrees  
atoms outside contour = 652, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model A (#32.1) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.36484420 -0.91715830 -0.16034147 275.00307794  
-0.79726014 0.21879492 0.56258783 164.15850506  
-0.48090019 0.33309077 -0.81103980 243.29869461  
Axis -0.55693597 0.77792142 0.29096492  
Axis point 211.66585714 0.00000000 70.85307433  
Rotation angle (degrees) 168.10988229  
Shift along axis 45.33469685  
  

> fitmap #32.2 inMap #18

Fit molecule COPI_cyto_J4027_model B (#32.2) to map
W20_J4027_consensus_resampled.mrc (#18) using 2426 atoms  
average map value = 0.354, steps = 64  
shifted from previous position = 0.279  
rotated from previous position = 0.915 degrees  
atoms outside contour = 634, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model B (#32.2) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.37575375 -0.90933745 -0.17864639 277.57875572  
-0.79848110 0.21984249 0.56044378 165.00984098  
-0.47035845 0.35323462 -0.80869540 240.85491140  
Axis -0.55315660 0.77874186 0.29593731  
Axis point 211.17574622 0.00000000 70.68321054  
Rotation angle (degrees) 169.20491693  
Shift along axis 46.23350389  
  

> fitmap #32.3 inMap #18

Fit molecule COPI_cyto_J4027_model C (#32.3) to map
W20_J4027_consensus_resampled.mrc (#18) using 1612 atoms  
average map value = 0.307, steps = 124  
shifted from previous position = 0.916  
rotated from previous position = 4.06 degrees  
atoms outside contour = 549, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model C (#32.3) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.38280043 -0.91660120 -0.11535204 274.19904393  
-0.75859054 0.24060781 0.60551491 157.21505378  
-0.52726108 0.31929633 -0.78742976 246.39824143  
Axis -0.54425835 0.78326479 0.30046485  
Axis point 211.53956724 0.00000000 67.39140608  
Rotation angle (degrees) 164.75519865  
Shift along axis 47.93990763  
  

> fitmap #32.4 inMap #18

Fit molecule COPI_cyto_J4027_model D (#32.4) to map
W20_J4027_consensus_resampled.mrc (#18) using 4745 atoms  
average map value = 0.2737, steps = 64  
shifted from previous position = 0.424  
rotated from previous position = 0.652 degrees  
atoms outside contour = 1745, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model D (#32.4) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.37438641 -0.91150980 -0.17024900 276.33175026  
-0.80075946 0.22523142 0.55502712 164.71539509  
-0.46756723 0.34412311 -0.81422367 240.98992687  
Axis -0.55358575 0.78040778 0.29070004  
Axis point 210.61143312 0.00000000 71.24312694  
Rotation angle (degrees) 169.01867576  
Shift along axis 45.62763928  
  

> fitmap #32.5 inMap #18

Fit molecule COPI_cyto_J4027_model E (#32.5) to map
W20_J4027_consensus_resampled.mrc (#18) using 1876 atoms  
average map value = 0.3307, steps = 48  
shifted from previous position = 0.367  
rotated from previous position = 3.19 degrees  
atoms outside contour = 589, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model E (#32.5) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.38890629 -0.90726627 -0.16006193 277.40112056  
-0.76465276 0.22097260 0.60537367 157.20851597  
-0.51386581 0.35782543 -0.77968129 242.84222727  
Axis -0.54436333 0.77802149 0.31360984  
Axis point 210.57407631 0.00000000 67.28775591  
Rotation angle (degrees) 166.85747662  
Shift along axis 47.46231881  
  

> fitmap #32.6 inMap #18

Fit molecule COPI_cyto_J4027_model F (#32.6) to map
W20_J4027_consensus_resampled.mrc (#18) using 2400 atoms  
average map value = 0.1739, steps = 100  
shifted from previous position = 2.11  
rotated from previous position = 17.6 degrees  
atoms outside contour = 2400, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model F (#32.6) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.22469468 -0.97442669 0.00222317 252.72099618  
-0.68062183 0.15857762 0.71526714 144.63194145  
-0.69732793 0.15920358 -0.69884762 265.52538785  
Axis -0.59112239 0.74365656 0.31232874  
Axis point 226.29273798 0.00000000 55.85483264  
Rotation angle (degrees) 151.94327126  
Shift along axis 41.09866330  
  

> ui tool show Matchmaker

> matchmaker #32.6 to #33

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_cyto_J4028_model, chain F (#33) with COPI_cyto_J4027_model F,
chain F (#32.6), sequence alignment score = 1592  
RMSD between 299 pruned atom pairs is 0.000 angstroms; (across all 299 pairs:
0.000)  
  

> hide #!32 models

> show #!32 models

> hide #!32 models

> hide #!18 models

> show #!20 models

> color #20 darkgrey models

> color #20 #a9a9a9c2 models

> show #!33 models

> split #33 chains

Split COPI_cyto_J4028_model (#33) into 13 models  
Chain information for COPI_cyto_J4028_model A #33.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J4028_model B #33.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J4028_model C #33.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J4028_model D #33.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J4028_model E #33.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J4028_model F #33.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J4028_model G #33.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J4028_model H #33.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J4028_model I #33.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J4028_model J #33.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J4028_model K #33.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J4028_model L #33.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J4028_model M #33.13  
---  
Chain | Description  
M | No description available  
  

> fitmap #33.1 inMap #20

Fit molecule COPI_cyto_J4028_model A (#33.1) to map
W20_J4028_consensus_resampled.mrc (#20) using 2590 atoms  
average map value = 0.3839, steps = 84  
shifted from previous position = 1.3  
rotated from previous position = 3.69 degrees  
atoms outside contour = 606, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model A (#33.1) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.42505705 -0.88684737 -0.18118571 281.77112295  
-0.78040543 0.25764379 0.56972543 159.62921913  
-0.45857812 0.38356412 -0.80161381 237.17247148  
Axis -0.53095306 0.79115444 0.30358443  
Axis point 206.86596376 0.00000000 70.78540234  
Rotation angle (degrees) 169.90338089  
Shift along axis 48.68599577  
  

> fitmap #33.2 inMap #20

Fit molecule COPI_cyto_J4028_model B (#33.2) to map
W20_J4028_consensus_resampled.mrc (#20) using 2426 atoms  
average map value = 0.3703, steps = 76  
shifted from previous position = 2  
rotated from previous position = 3.77 degrees  
atoms outside contour = 594, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model B (#33.2) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.42163847 -0.88604192 -0.19274527 282.36522569  
-0.78360399 0.24908325 0.56914176 161.05650807  
-0.45627383 0.39100801 -0.79932906 236.28096107  
Axis -0.53305638 0.78859614 0.30654042  
Axis point 207.42054850 0.00000000 70.38397992  
Rotation angle (degrees) 170.38149718  
Shift along axis 48.92162012  
  

> fitmap #33.3 inMap #20

Fit molecule COPI_cyto_J4028_model C (#33.3) to map
W20_J4028_consensus_resampled.mrc (#20) using 1612 atoms  
average map value = 0.2936, steps = 120  
shifted from previous position = 1.59  
rotated from previous position = 5.86 degrees  
atoms outside contour = 556, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model C (#33.3) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.38874794 -0.91700982 -0.08926390 273.70817090  
-0.74150605 0.25389180 0.62105374 153.76404568  
-0.54684900 0.30762308 -0.77866824 247.74574422  
Axis -0.53877892 0.78657655 0.30168628  
Axis point 211.55093832 0.00000000 66.06733162  
Rotation angle (degrees) 163.08987268  
Shift along axis 48.22049311  
  

> fitmap #33.4 inMap #20

Fit molecule COPI_cyto_J4028_model D (#33.4) to map
W20_J4028_consensus_resampled.mrc (#20) using 4745 atoms  
average map value = 0.2743, steps = 52  
shifted from previous position = 0.325  
rotated from previous position = 2.63 degrees  
atoms outside contour = 1777, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model D (#33.4) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.35425466 -0.92574203 -0.13230776 272.21729531  
-0.80879167 0.23228423 0.54027779 166.54524500  
-0.46942484 0.29840534 -0.83102021 247.09025195  
Axis -0.56108841 0.78203404 0.27129791  
Axis point 212.23977312 0.00000000 73.93457988  
Rotation angle (degrees) 167.55287093  
Shift along axis 44.54114989  
  

> fitmap #33.5 inMap #20

Fit molecule COPI_cyto_J4028_model E (#33.5) to map
W20_J4028_consensus_resampled.mrc (#20) using 1876 atoms  
average map value = 0.3337, steps = 68  
shifted from previous position = 0.86  
rotated from previous position = 3.26 degrees  
atoms outside contour = 607, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model E (#33.5) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.40812036 -0.89487089 -0.18067614 280.82990976  
-0.77162408 0.23236180 0.59211848 158.56716868  
-0.48788736 0.38106967 -0.78533550 239.27651010  
Axis -0.53761002 0.78256694 0.31394976  
Axis point 209.07381918 0.00000000 68.40687366  
Rotation angle (degrees) 168.68024136  
Shift along axis 48.23325430  
  

> fitmap #33.10 inMap #20

Fit molecule COPI_cyto_J4028_model J (#33.10) to map
W20_J4028_consensus_resampled.mrc (#20) using 1112 atoms  
average map value = 0.2746, steps = 88  
shifted from previous position = 1.18  
rotated from previous position = 6.07 degrees  
atoms outside contour = 487, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model J (#33.10) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.37976892 -0.92311743 -0.06024771 266.93454127  
-0.77672422 0.28281318 0.56277545 158.41114514  
-0.50246898 0.26052048 -0.82441132 252.69246283  
Axis -0.54431763 0.79637675 0.26363308  
Axis point 208.95699781 0.00000000 74.09614523  
Rotation angle (degrees) 163.88025316  
Shift along axis 47.47586703  
  

> fitmap #33.12 inMap #20

Fit molecule COPI_cyto_J4028_model L (#33.12) to map
W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms  
average map value = 0.2305, steps = 152  
shifted from previous position = 15.6  
rotated from previous position = 25.9 degrees  
atoms outside contour = 812, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model L (#33.12) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.06107414 -0.89318761 -0.44551751 275.05032468  
-0.79982244 -0.22322988 0.55718265 197.31395144  
-0.59712146 0.39036435 -0.70075791 230.69793847  
Axis -0.68372085 0.62136335 0.38266615  
Axis point 0.00000000 233.57747065 184.11991319  
Rotation angle (degrees) 172.99286255  
Shift along axis 22.82630694  
  

> select add #33.12

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> view matrix models
> #33.12,-0.71047,-0.45523,-0.53665,342.29,-0.62968,0.75173,0.19595,130.11,0.31422,0.47714,-0.82074,104.42

> view matrix models
> #33.12,-0.87976,-0.194,-0.43403,328.35,-0.31813,0.91866,0.23421,62.94,0.35329,0.34413,-0.86992,118.06

> fitmap #33.12 inMap #20

Fit molecule COPI_cyto_J4028_model L (#33.12) to map
W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms  
average map value = 0.219, steps = 148  
shifted from previous position = 4.64  
rotated from previous position = 34.8 degrees  
atoms outside contour = 813, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model L (#33.12) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.65509662 -0.64625356 -0.39141380 328.46645180  
-0.75535360 0.57185725 0.32003163 147.76949721  
0.01701124 0.50530746 -0.86277170 152.27605950  
Axis 0.40140909 -0.88487271 -0.23637052  
Axis point 188.23063104 0.00000000 79.03730027  
Rotation angle (degrees) 166.65689588  
Shift along axis -34.90134836  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #33.12,-0.03029,-0.7598,0.64945,102.21,-0.99925,0.0072683,-0.038101,287,0.024229,-0.65012,-0.75945,246.16

> fitmap #33.12 inMap #20

Fit molecule COPI_cyto_J4028_model L (#33.12) to map
W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms  
average map value = 0.2032, steps = 160  
shifted from previous position = 13.1  
rotated from previous position = 20.8 degrees  
atoms outside contour = 909, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model L (#33.12) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
0.16998318 -0.52866209 0.83163822 33.05834902  
-0.98535039 -0.07936651 0.15094897 271.66299549  
-0.01379677 -0.84511382 -0.53440836 228.58308709  
Axis -0.71969674 0.61086190 -0.32997627  
Axis point 0.00000000 219.83009454 42.24482979  
Rotation angle (degrees) 136.21122723  
Shift along axis 66.72959442  
  

> ui mousemode right "translate selected models"

> view matrix models
> #33.12,0.16998,-0.52866,0.83164,40.813,-0.98535,-0.079367,0.15095,266.5,-0.013797,-0.84511,-0.53441,239.35

> ui mousemode right "rotate selected models"

> view matrix models
> #33.12,-0.43029,-0.87383,0.22644,246.31,-0.87355,0.46631,0.13952,199.93,-0.22751,-0.13778,-0.96398,263.72

> ui mousemode right "translate selected models"

> view matrix models
> #33.12,-0.43029,-0.87383,0.22644,240.63,-0.87355,0.46631,0.13952,199.48,-0.22751,-0.13778,-0.96398,257.34

> fitmap #33.12 inMap #20

Fit molecule COPI_cyto_J4028_model L (#33.12) to map
W20_J4028_consensus_resampled.mrc (#20) using 1420 atoms  
average map value = 0.259, steps = 136  
shifted from previous position = 2.22  
rotated from previous position = 19 degrees  
atoms outside contour = 643, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model L (#33.12) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.11376158 -0.96773135 0.22484296 202.04835591  
-0.96542922 0.16110229 0.20492070 231.97393999  
-0.23453090 -0.19375786 -0.95260336 262.84035133  
Axis -0.65544634 0.75523227 0.00378481  
Axis point 228.77213631 0.00000000 107.04713970  
Rotation angle (degrees) 162.29431769  
Shift along axis 43.75715061  
  

> select subtract #33.12

Nothing selected  

> fitmap #33.13 inMap #20

Fit molecule COPI_cyto_J4028_model M (#33.13) to map
W20_J4028_consensus_resampled.mrc (#20) using 4552 atoms  
average map value = 0.2597, steps = 164  
shifted from previous position = 11.9  
rotated from previous position = 21.2 degrees  
atoms outside contour = 2429, contour level = 0.25474  
  
Position of COPI_cyto_J4028_model M (#33.13) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.41064746 -0.90764367 0.08690026 262.06407158  
-0.84733447 0.41507760 0.33126258 174.12202496  
-0.33673873 0.06239856 -0.93952832 256.95292530  
Axis -0.53201816 0.83828111 0.11933760  
Axis point 205.62822196 0.00000000 94.49206914  
Rotation angle (degrees) 165.36365713  
Shift along axis 37.20450278  
  

> show #!32 models

> hide #!33 models

> hide #!32 models

> show #!33 models

> hide #!33 models

> split #34 chains

Split COPI_cyto_J3988_model (#34) into 13 models  
Chain information for COPI_cyto_J3988_model A #34.1  
---  
Chain | Description  
A | No description available  
  
Chain information for COPI_cyto_J3988_model B #34.2  
---  
Chain | Description  
B | No description available  
  
Chain information for COPI_cyto_J3988_model C #34.3  
---  
Chain | Description  
C | No description available  
  
Chain information for COPI_cyto_J3988_model D #34.4  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_cyto_J3988_model E #34.5  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_cyto_J3988_model F #34.6  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_cyto_J3988_model G #34.7  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_cyto_J3988_model H #34.8  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_cyto_J3988_model I #34.9  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_cyto_J3988_model J #34.10  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_cyto_J3988_model K #34.11  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_cyto_J3988_model L #34.12  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_cyto_J3988_model M #34.13  
---  
Chain | Description  
M | No description available  
  

> show #34.1 models

> show #34.2 models

> show #34.3 models

> show #!34.4 models

> show #34.5 models

> show #34.6 models

> show #34.7 models

> show #34.8 models

> show #34.9 models

> show #34.10 models

> show #34.11 models

> show #34.12 models

> show #34.13 models

> hide #!20 models

> show #!22 models

> color #22 darkgrey models

> color #22 #a9a9a9bf models

> fitmap #34.1 inMap #22

Fit molecule COPI_cyto_J3988_model A (#34.1) to map
W20_J3988_consensus_resampled.mrc (#22) using 2590 atoms  
average map value = 0.3688, steps = 88  
shifted from previous position = 1.25  
rotated from previous position = 3.5 degrees  
atoms outside contour = 749, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model A (#34.1) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.41785370 -0.88839960 -0.19011695 282.28257009  
-0.78880679 0.25093956 0.56108217 162.05511406  
-0.45075731 0.38441580 -0.80563165 235.85823021  
Axis -0.53495212 0.78922836 0.30157060  
Axis point 207.72235198 0.00000000 70.74799729  
Rotation angle (degrees) 170.49558915  
Shift along axis 48.01874106  
  

> fitmap #34.2 inMap #22

Fit molecule COPI_cyto_J3988_model B (#34.2) to map
W20_J3988_consensus_resampled.mrc (#22) using 2426 atoms  
average map value = 0.3348, steps = 104  
shifted from previous position = 1.68  
rotated from previous position = 3.88 degrees  
atoms outside contour = 828, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model B (#34.2) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.42101840 -0.88538396 -0.19707555 283.10669504  
-0.78443773 0.24632045 0.56919566 160.85163308  
-0.45541296 0.39423534 -0.79823402 235.48770247  
Axis -0.53352603 0.78777711 0.30782658  
Axis point 207.58242660 0.00000000 70.13942680  
Rotation angle (degrees) 170.56282406  
Shift along axis 48.15981832  
  

> fitmap #34.3 inMap #22

Fit molecule COPI_cyto_J3988_model C (#34.3) to map
W20_J3988_consensus_resampled.mrc (#22) using 1612 atoms  
average map value = 0.3235, steps = 80  
shifted from previous position = 1.01  
rotated from previous position = 1.39 degrees  
atoms outside contour = 647, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model C (#34.3) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.38953007 -0.90460759 -0.17306487 278.08945587  
-0.79075902 0.23214543 0.56639976 162.53472037  
-0.47219330 0.35748234 -0.80575423 240.06559363  
Axis -0.54660128 0.78262495 0.29786781  
Axis point 209.73775516 0.00000000 70.39505904  
Rotation angle (degrees) 168.98267188  
Shift along axis 46.70748572  
  

> fitmap #34.4 inMap #22

Fit molecule COPI_cyto_J3988_model D (#34.4) to map
W20_J3988_consensus_resampled.mrc (#22) using 4745 atoms  
average map value = 0.341, steps = 72  
shifted from previous position = 0.451  
rotated from previous position = 2.53 degrees  
atoms outside contour = 1760, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model D (#34.4) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.35609850 -0.92473928 -0.13435451 272.54654270  
-0.80894027 0.23309315 0.53970662 166.76836324  
-0.46777080 0.30087349 -0.83106296 247.02887626  
Axis -0.56042334 0.78236325 0.27172306  
Axis point 212.17904341 0.00000000 74.04958983  
Rotation angle (degrees) 167.69692699  
Shift along axis 44.85543655  
  

> fitmap #34.5 inMap #22

Fit molecule COPI_cyto_J3988_model E (#34.5) to map
W20_J3988_consensus_resampled.mrc (#22) using 1876 atoms  
average map value = 0.3399, steps = 68  
shifted from previous position = 0.902  
rotated from previous position = 1.88 degrees  
atoms outside contour = 644, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model E (#34.5) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.38559316 -0.90595853 -0.17480580 278.32647192  
-0.80563868 0.23824013 0.54239099 166.10780051  
-0.44973798 0.34997256 -0.82173899 240.13441550  
Axis -0.54937100 0.78495483 0.28642174  
Axis point 210.04384962 0.00000000 72.68833745  
Rotation angle (degrees) 169.91400249  
Shift along axis 46.26234424  
  

> fitmap #34.10 inMap #22

Fit molecule COPI_cyto_J3988_model J (#34.10) to map
W20_J3988_consensus_resampled.mrc (#22) using 1112 atoms  
average map value = 0.314, steps = 56  
shifted from previous position = 0.967  
rotated from previous position = 5.85 degrees  
atoms outside contour = 470, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model J (#34.10) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.37577208 -0.92422463 -0.06785421 266.88773036  
-0.79027325 0.28134549 0.54434632 161.90561717  
-0.48400780 0.25817351 -0.83611178 252.25402649  
Axis -0.54768370 0.79644372 0.25635904  
Axis point 209.14918816 0.00000000 75.62770199  
Rotation angle (degrees) 164.85531677  
Shift along axis 47.44625196  
  

> fitmap #34.12 inMap #22

Fit molecule COPI_cyto_J3988_model L (#34.12) to map
W20_J3988_consensus_resampled.mrc (#22) using 1420 atoms  
average map value = 0.2477, steps = 128  
shifted from previous position = 15.9  
rotated from previous position = 23.9 degrees  
atoms outside contour = 825, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model L (#34.12) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.13744140 -0.87706877 -0.46028280 286.39333689  
-0.79755718 -0.17757218 0.57651599 190.01595705  
-0.58737759 0.44633901 -0.67510671 220.17263411  
Axis -0.65564558 0.64012190 0.40046576  
Axis point 0.00000000 242.83430967 190.87489306  
Rotation angle (degrees) 174.30264049  
Shift along axis 22.03245138  
  

> ui mousemode right "rotate selected models"

> select add #34.12

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> view matrix models
> #34.12,0.094052,-0.95592,0.27815,157.02,-0.86993,0.056954,0.48988,190.57,-0.48413,-0.28805,-0.82622,295.38

> fitmap #34.12 inMap #22

Fit molecule COPI_cyto_J3988_model L (#34.12) to map
W20_J3988_consensus_resampled.mrc (#22) using 1420 atoms  
average map value = 0.265, steps = 180  
shifted from previous position = 7.48  
rotated from previous position = 16.7 degrees  
atoms outside contour = 709, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model L (#34.12) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.10354097 -0.97915690 0.17473139 207.46054459  
-0.94372455 0.15219348 0.29363435 218.75648454  
-0.31410708 -0.13449511 -0.93981265 267.23328820  
Axis -0.65787226 0.75115891 0.05444605  
Axis point 229.01761440 0.00000000 99.48866389  
Rotation angle (degrees) 161.01082491  
Shift along axis 42.38814162  
  

> select subtract #34.12

Nothing selected  

> fitmap #34.13 inMap #22

Fit molecule COPI_cyto_J3988_model M (#34.13) to map
W20_J3988_consensus_resampled.mrc (#22) using 4552 atoms  
average map value = 0.2757, steps = 176  
shifted from previous position = 11.7  
rotated from previous position = 23.1 degrees  
atoms outside contour = 2512, contour level = 0.28583  
  
Position of COPI_cyto_J3988_model M (#34.13) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.23360378 -0.97224105 0.01329047 246.50433978  
-0.93813795 0.22896058 0.25975806 213.83868979  
-0.25559044 0.04821217 -0.96558227 246.39586728  
Axis -0.61528240 0.78204162 0.09918904  
Axis point 220.79513963 0.00000000 94.62595818  
Rotation angle (degrees) 170.10113474  
Shift along axis 40.00074310  
  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_29/denmod_map.ccp4

Opened denmod_map.ccp4 as #35, grid size 99,98,133, pixel 1.19, shown at level
0.318, step 1, values float32  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_30/denmod_map.ccp4

Opened denmod_map.ccp4 as #36, grid size 97,98,137, pixel 1.19, shown at level
0.404, step 1, values float32  

> hide #!34 models

> hide #!22 models

> hide #!36 models

> volume #35 level 0.105

> show #!34 models

> hide #!35 models

> show #!36 models

> volume #36 level 0.1681

> hide #!36 models

> close #35-36

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_29/denmod_map.ccp4

Opened denmod_map.ccp4 as #35, grid size 99,98,133, pixel 1.19, shown at level
0.318, step 1, values float32  

> close #35

> show #!47 models

> hide #!47 models

> close #56#47-55,57

> show #!94 models

> hide #!94 models

> close #71-72,76,78-80,83,86-88#58-70,73-75,77,81-82,84-85,89-95

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/COPI_soluble_job155_dhelix.pdb"

Chain information for COPI_soluble_job155_dhelix.pdb #35  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/COPI_soluble_job160_dhelix.pdb"

Chain information for COPI_soluble_job160_dhelix.pdb #36  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
  

> ui tool show Matchmaker

> matchmaker #!35-36 to #34.4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_cyto_J3988_model D, chain D (#34.4) with
COPI_soluble_job155_dhelix.pdb, chain I (#35), sequence alignment score = 1535  
RMSD between 291 pruned atom pairs is 0.541 angstroms; (across all 305 pairs:
0.988)  
  
Matchmaker COPI_cyto_J3988_model D, chain D (#34.4) with
COPI_soluble_job160_dhelix.pdb, chain I (#36), sequence alignment score = 1538  
RMSD between 291 pruned atom pairs is 0.541 angstroms; (across all 305 pairs:
0.988)  
  

> hide #34.1-3,5-13#!35-36#!34.4 atoms

> show #34.1-3,5-13#!35-36#!34.4 cartoons

> hide #!34 models

> hide #!36 models

> show #!16 models

> show #!18 models

> hide #!16 models

> hide #!18 models

> show #!20 models

> hide #!20 models

> show #!22 models

> hide #!35 models

> show #!36 models

> show #!20 models

> hide #!20 models

> show #!18 models

> hide #!22 models

> hide #!18 models

> hide #!36 models

> split #35 chains

Split COPI_soluble_job155_dhelix.pdb (#35) into 14 models  
Chain information for COPI_soluble_job155_dhelix.pdb D #35.1  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb E #35.2  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb F #35.3  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb G #35.4  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb H #35.5  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb I #35.6  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb J #35.7  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb K #35.8  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb L #35.9  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb M #35.10  
---  
Chain | Description  
M | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb N #35.11  
---  
Chain | Description  
N | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb O #35.12  
---  
Chain | Description  
O | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb P #35.13  
---  
Chain | Description  
P | No description available  
  
Chain information for COPI_soluble_job155_dhelix.pdb Q #35.14  
---  
Chain | Description  
Q | No description available  
  

> split #36 chains

Split COPI_soluble_job160_dhelix.pdb (#36) into 14 models  
Chain information for COPI_soluble_job160_dhelix.pdb D #36.1  
---  
Chain | Description  
D | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb E #36.2  
---  
Chain | Description  
E | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb F #36.3  
---  
Chain | Description  
F | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb G #36.4  
---  
Chain | Description  
G | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb H #36.5  
---  
Chain | Description  
H | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb I #36.6  
---  
Chain | Description  
I | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb J #36.7  
---  
Chain | Description  
J | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb K #36.8  
---  
Chain | Description  
K | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb L #36.9  
---  
Chain | Description  
L | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb M #36.10  
---  
Chain | Description  
M | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb N #36.11  
---  
Chain | Description  
N | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb O #36.12  
---  
Chain | Description  
O | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb P #36.13  
---  
Chain | Description  
P | No description available  
  
Chain information for COPI_soluble_job160_dhelix.pdb Q #36.14  
---  
Chain | Description  
Q | No description available  
  

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/ResolveCryoEM_32/J4028_denmod_map.ccp4

Opened J4028_denmod_map.ccp4 as #37, grid size 98,99,135, pixel 1.19, shown at
level 0.424, step 1, values float32  

> volume #37 level 0.2276

> hide #!35 models

> hide #!36 models

> show #!35.14 models

> show #!35.13 models

> show #35.12 models

> show #!35.11 models

> show #35.10 models

> show #35.9 models

> show #35.8 models

> show #!35.7 models

> show #!35.6 models

> show #35.5 models

> show #35.4 models

> show #35.3 models

> show #35.2 models

> show #35.1 models

> hide #!35 models

> volume #37 level 0.1206

> close #37

> show #!16 models

> show #!31 models

> show #!35 models

> hide #35.1 models

> hide #35.2 models

> hide #35.3 models

> hide #35.4 models

> hide #35.5 models

> hide #!35.6 models

> hide #!35.7 models

> hide #35.8 models

> hide #35.9 models

> show #35.9 models

> hide #35.10 models

> show #35.10 models

> hide #35.10 models

> show #35.10 models

> hide #!35.11 models

> show #!35.11 models

> hide #35.12 models

> hide #!35.13 models

> hide #!35.14 models

> fitmap #35.9 inMap #16

Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
W20_J4026_consensus_resampled.mrc (#16) using 1163 atoms  
average map value = 0.3245, steps = 56  
shifted from previous position = 1.07  
rotated from previous position = 3.98 degrees  
atoms outside contour = 440, contour level = 0.25963  
  
Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.90987894 0.24236896 -0.33671591 435.50395252  
0.06606031 -0.71661672 -0.69433170 604.82381864  
-0.40958070 -0.65400135 0.63602349 262.39041137  
Axis 0.20683441 0.37368744 -0.90419977  
Axis point 263.30917938 345.30538105 0.00000000  
Rotation angle (degrees) 174.40510072  
Shift along axis 78.83891898  
  

> fitmap #35.10 inMap #16

Fit molecule COPI_soluble_job155_dhelix.pdb M (#35.10) to map
W20_J4026_consensus_resampled.mrc (#16) using 2212 atoms  
average map value = 0.3306, steps = 92  
shifted from previous position = 2.46  
rotated from previous position = 6.1 degrees  
atoms outside contour = 710, contour level = 0.25963  
  
Position of COPI_soluble_job155_dhelix.pdb M (#35.10) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.91287694 0.27628102 -0.30054033 410.29266882  
-0.00773154 -0.74776328 -0.66392040 629.67159952  
-0.40816163 -0.60375398 0.68475193 227.42100406  
Axis 0.19432248 0.34758987 -0.91728952  
Axis point 254.63604518 341.25031476 0.00000000  
Rotation angle (degrees) 171.09417945  
Shift along axis 89.98565405  
  

> fitmap #35.11 inMap #16

Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
W20_J4026_consensus_resampled.mrc (#16) using 1064 atoms  
average map value = 0.3024, steps = 52  
shifted from previous position = 1.19  
rotated from previous position = 1.61 degrees  
atoms outside contour = 298, contour level = 0.25963  
  
Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.93792901 0.21017775 -0.27588855 435.11677592  
0.06068204 -0.68374702 -0.72719166 606.90260953  
-0.34147748 -0.69879563 0.62855215 261.30949009  
Axis 0.17136788 0.39582419 -0.90219524  
Axis point 255.61353944 351.07885546 0.00000000  
Rotation angle (degrees) 175.24753470  
Shift along axis 79.03959464  
  

> hide #31.13 models

> hide #31.12 models

> show #31.12 models

> select add #31.12

1420 atoms, 1441 bonds, 177 residues, 1 model selected  

> view matrix models
> #31.12,-0.23372,-0.97024,-0.063385,254.71,-0.96642,0.23897,-0.094492,266.72,0.10683,0.039172,-0.99351,199.68

> fitmap #31.12 inMap #16

Fit molecule COPI_cyto_J4026_model L (#31.12) to map
W20_J4026_consensus_resampled.mrc (#16) using 1420 atoms  
average map value = 0.2882, steps = 136  
shifted from previous position = 4.88  
rotated from previous position = 24.5 degrees  
atoms outside contour = 593, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model L (#31.12) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.11780824 -0.96709435 0.22549890 202.70773070  
-0.96549277 0.16465999 0.20176923 232.00719445  
-0.23226052 -0.19394747 -0.95312090 262.37235731  
Axis -0.65397629 0.75651041 0.00264684  
Axis point 228.48470686 0.00000000 107.10492224  
Rotation angle (degrees) 162.38937332  
Shift along axis 43.64426578  
  

> select subtract #31.12

Nothing selected  

> show #31.13 models

> hide #31.13 models

> hide #31.12 models

> hide #31.11 models

> hide #31.10 models

> hide #31.9 models

> hide #31.8 models

> hide #31.7 models

> hide #31.6 models

> hide #31.5 models

> hide #!31.4 models

> hide #31.3 models

> hide #31.2 models

> hide #31.1 models

> hide #!16 models

> show #31.13 models

> hide #35.9 models

> hide #!35.11 models

> hide #35.10 models

> ui mousemode right select

Drag select of 228 residues  

> select up

2019 atoms, 2046 bonds, 257 residues, 1 model selected  

> delete sel

> show #35.10 models

Drag select of 6 residues, 1 pseudobonds  

> select up

61 atoms, 60 bonds, 1 pseudobond, 8 residues, 2 models selected  

> delete sel

Drag select of 3 residues  

> select up

130 atoms, 130 bonds, 17 residues, 1 model selected  

> delete sel

> fitmap #31.13 inMap #16

Fit molecule COPI_cyto_J4026_model M (#31.13) to map
W20_J4026_consensus_resampled.mrc (#16) using 2342 atoms  
average map value = 0.3254, steps = 72  
shifted from previous position = 2.25  
rotated from previous position = 5.92 degrees  
atoms outside contour = 789, contour level = 0.25963  
  
Position of COPI_cyto_J4026_model M (#31.13) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.14741636 -0.97480443 0.16740596 215.74618933  
-0.97007287 0.17551559 0.16778831 236.68236999  
-0.19294315 -0.13766124 -0.97150519 252.55946622  
Axis -0.64657421 0.76278534 0.01001574  
Axis point 227.98326837 0.00000000 105.57175219  
Rotation angle (degrees) 166.33727095  
Shift along axis 43.57149027  
  

> hide #!31.13 models

> show #!31.13 models

> show #!16 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_20250401_ct_alpha1_350_gamma1_350/fold_20250401_ct_alpha1_350_gamma1_350_model_0.cif"

Chain information for fold_20250401_ct_alpha1_350_gamma1_350_model_0.cif #37  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #37 to #31.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_cyto_J4026_model A, chain A (#31.1) with
fold_20250401_ct_alpha1_350_gamma1_350_model_0.cif, chain A (#37), sequence
alignment score = 1357.6  
RMSD between 278 pruned atom pairs is 0.471 angstroms; (across all 313 pairs:
6.653)  
  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_20250401_ct_alpha1_350_gamma1_50/fold_20250401_ct_alpha1_350_gamma1_50_model_0.cif"

Chain information for fold_20250401_ct_alpha1_350_gamma1_50_model_0.cif #38  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #38 to #24.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_cyto_for_J4027_v1 A, chain A (#24.1) with
fold_20250401_ct_alpha1_350_gamma1_50_model_0.cif, chain A (#38), sequence
alignment score = 1354  
RMSD between 279 pruned atom pairs is 0.445 angstroms; (across all 313 pairs:
6.676)  
  

> hide #!16 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Alphafold
> predictions/fold_2025_01_17_alpha1_330gamma1_330zeta/fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif"

Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif #39  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #39 to #24.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COPI_cyto_for_J4027_v1 A, chain A (#24.1) with
fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif, chain B (#39), sequence
alignment score = 1688.7  
RMSD between 283 pruned atom pairs is 0.307 angstroms; (across all 318 pairs:
4.917)  
  

> hide #38 models

> hide #37 models

> fitmap #39 inMap #16

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#39) to map
W20_J4026_consensus_resampled.mrc (#16) using 6676 atoms  
average map value = 0.2973, steps = 112  
shifted from previous position = 5.99  
rotated from previous position = 14.7 degrees  
atoms outside contour = 2828, contour level = 0.25963  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#39)
relative to W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
0.75236864 0.61844958 -0.22685138 135.89900591  
0.54481378 -0.77776674 -0.31345947 141.53555984  
-0.37029633 0.11224532 -0.92210716 89.13598609  
Axis 0.93516725 0.31511280 -0.16175949  
Axis point 0.00000000 40.80728347 61.99249889  
Rotation angle (degrees) 166.84366143  
Shift along axis 157.26937502  
  

> split #39 chains

Split fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif (#39) into 3 models  
Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A
#39.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif B
#39.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif C
#39.3  
---  
Chain | Description  
C | No description available  
  

> show #!16 models

> hide #!31.13 models

> hide #39.2 models

> show #39.2 models

> hide #39.2 models

> hide #39.1 models

> show #39.1 models

> hide #39.3 models

> show #31.12 models

> show #31.1 models

> fitmap #39.1 inMap #16

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4026_consensus_resampled.mrc (#16) using 2567 atoms  
average map value = 0.332, steps = 92  
shifted from previous position = 1.08  
rotated from previous position = 8.07 degrees  
atoms outside contour = 837, contour level = 0.25963  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
0.83404122 0.50639742 -0.21894494 135.37114526  
0.43420964 -0.84733835 -0.30574452 138.37406207  
-0.34034868 0.15993553 -0.92659775 89.77783066  
Axis 0.95695074 0.24947901 -0.14834252  
Axis point 0.00000000 44.30433155 61.88415197  
Rotation angle (degrees) 165.91774988  
Shift along axis 150.74707237  
  

> hide #!16 models

> hide #31.12 models

> show #35.9 models

> hide #35.9 models

> show #35.9 models

> show #!16 models

> hide #!16 models

> hide #35.9 models

> hide #35.10 models

> show #35.9 models

> hide #39.1 models

Drag select of 11 residues  

> select up

130 atoms, 130 bonds, 17 residues, 1 model selected  

> delete sel

> show #39.1 models

> select #35.9/L:317

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> hide #39.1 models

Drag select of 4 residues  

> delete sel

Drag select of 5 residues  

> delete sel

> select #35.9/L:327

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> show #39.1 models

> hide #39.1 models

> select #35.9/L:328

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #35.9/L:329

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> show #39.1 models

> select #35.9/L:330

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> show #!16 models

> fitmap #35.9 inMap #16

Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
W20_J4026_consensus_resampled.mrc (#16) using 930 atoms  
average map value = 0.3516, steps = 52  
shifted from previous position = 0.499  
rotated from previous position = 6.25 degrees  
atoms outside contour = 295, contour level = 0.25963  
  
Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
W20_J4026_consensus_resampled.mrc (#16) coordinates:  
Matrix rotation and translation  
-0.93642912 0.16612187 -0.30903727 462.34398677  
0.11986381 -0.67634146 -0.72677018 585.05727704  
-0.32974714 -0.71761114 0.61343384 270.00020679  
Axis 0.17783383 0.40210728 -0.89815637  
Axis point 261.88005557 349.74957427 0.00000000  
Rotation angle (degrees) 178.52437469  
Shift along axis 74.97378580  
  

> show #35.8 models

> hide #35.8 models

> show #!35.11 models

> show #31.12 models

> show #31.11 models

> show #31.10 models

> show #31.9 models

> show #31.8 models

> show #31.7 models

> show #31.6 models

> show #31.5 models

> show #!31.4 models

> show #31.3 models

> show #31.2 models

> combine #31.1 #31.2 #31.3 #31.4 #31.5 #31.6 #31.7 #31.8 #31.9 #31.10 #31.11
> #31.12 #39.1 #35.9 #35.11

Remapping chain ID 'A' in fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif
A #39.1 to 'M'  
Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N'  
Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O'  

> rename #40 COPI_cyto_J4026_model

> hide #!40 models

> show #!40 models

> hide #!40 models

> hide #!16 models

> show #!18 models

> fitmap #35.11 inMap #18

Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
W20_J4027_consensus_resampled.mrc (#18) using 1064 atoms  
average map value = 0.345, steps = 52  
shifted from previous position = 0.96  
rotated from previous position = 4.13 degrees  
atoms outside contour = 305, contour level = 0.25259  
  
Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.95797163 0.17569317 -0.22676476 434.71371371  
0.05774245 -0.65621750 -0.75235923 607.00290226  
-0.28099138 -0.73383275 0.61849280 258.09556438  
Axis 0.14127895 0.41352064 -0.89946703  
Axis point 248.09458414 355.10604389 0.00000000  
Rotation angle (degrees) 176.24059016  
Shift along axis 80.27567222  
  

> fitmap #35.9 inMap #18

Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
W20_J4027_consensus_resampled.mrc (#18) using 930 atoms  
average map value = 0.3717, steps = 64  
shifted from previous position = 4.09  
rotated from previous position = 12 degrees  
atoms outside contour = 279, contour level = 0.25259  
  
Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.98236672 0.03849512 -0.18295835 476.12367349  
0.12352589 -0.60093803 -0.78969288 580.42963487  
-0.14034595 -0.79836809 0.58558637 250.87293860  
Axis -0.09083469 -0.44617724 0.89032293  
Axis point 243.54419066 359.36795920 0.00000000  
Rotation angle (degrees) 177.26292686  
Shift along axis -78.86510835  
  

> fitmap #39.1 inMap #18

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4027_consensus_resampled.mrc (#18) using 2567 atoms  
average map value = 0.2497, steps = 140  
shifted from previous position = 20.2  
rotated from previous position = 23.5 degrees  
atoms outside contour = 1358, contour level = 0.25259  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
0.71011541 0.46894974 -0.52518782 133.17594101  
0.50811821 -0.85767517 -0.07879844 140.50399717  
-0.48739306 -0.21090151 -0.84733026 102.37727978  
Axis -0.92459305 -0.26452658 0.27414118  
Axis point 0.00000000 53.88234017 68.89098797  
Rotation angle (degrees) 175.90338628  
Shift along axis -132.23476323  
  

> select add #39.1

2567 atoms, 2609 bonds, 330 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #39.1,0.71012,0.46895,-0.52519,127.98,0.50812,-0.85768,-0.078798,150.01,-0.48739,-0.2109,-0.84733,99.315

> fitmap #39.1 inMap #18

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4027_consensus_resampled.mrc (#18) using 2567 atoms  
average map value = 0.2908, steps = 104  
shifted from previous position = 3.89  
rotated from previous position = 15.2 degrees  
atoms outside contour = 938, contour level = 0.25259  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
0.65350179 0.33145691 -0.68049373 127.41590893  
0.52879246 -0.84317616 0.09712103 144.98236935  
-0.54158466 -0.42330872 -0.72628905 97.39971457  
Axis -0.90721165 -0.24214590 0.34399476  
Axis point 0.00000000 66.60547701 63.44217524  
Rotation angle (degrees) 163.33177472  
Shift along axis -117.19509172  
  

> hide #31.12 models

> hide #!31 models

> show #!32 models

> hide #32.13 models

> fitmap #32.12 inMap #18

Fit molecule COPI_cyto_J4027_model L (#32.12) to map
W20_J4027_consensus_resampled.mrc (#18) using 1420 atoms  
average map value = 0.249, steps = 84  
shifted from previous position = 0.209  
rotated from previous position = 0.257 degrees  
atoms outside contour = 664, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model L (#32.12) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.36763985 -0.91576410 -0.16191685 275.33631018  
-0.79632880 0.22007538 0.56340686 164.04444754  
-0.48031386 0.33606986 -0.81015780 242.91724000  
Axis -0.55576549 0.77837779 0.29198072  
Axis point 211.47624167 0.00000000 70.72859152  
Rotation angle (degrees) 168.19824647  
Shift along axis 45.59328469  
  

> view matrix models
> #39.1,0.6535,0.33146,-0.68049,127.38,0.52879,-0.84318,0.097121,144.98,-0.54158,-0.42331,-0.72629,97.387

> select subtract #39.1

Nothing selected  

> fitmap #32.5 inMap #18

Fit molecule COPI_cyto_J4027_model E (#32.5) to map
W20_J4027_consensus_resampled.mrc (#18) using 1876 atoms  
average map value = 0.3307, steps = 28  
shifted from previous position = 0.0226  
rotated from previous position = 0.025 degrees  
atoms outside contour = 588, contour level = 0.25259  
  
Position of COPI_cyto_J4027_model E (#32.5) relative to
W20_J4027_consensus_resampled.mrc (#18) coordinates:  
Matrix rotation and translation  
-0.38917297 -0.90711538 -0.16026883 277.45394634  
-0.76472866 0.22115752 0.60521025 157.23067335  
-0.51355087 0.35809364 -0.77976565 242.80657971  
Axis -0.54426642 0.77809236 0.31360219  
Axis point 210.56184964 0.00000000 67.30315702  
Rotation angle (degrees) 166.87842423  
Shift along axis 47.47579529  
  

> combine #32.1 #32.2 #32.3 #32.4 #32.5 #32.6 #32.7 #32.8 #32.9 #32.10 #32.11
> #32.12 #39.1 #35.9 #35.11

Remapping chain ID 'A' in fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif
A #39.1 to 'M'  
Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N'  
Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O'  

> rename #41 COPI_cyto_J4017_model

> hide #39.1 models

> show #39.1 models

> hide #!41 models

> hide #!32 models

> hide #!18 models

> show #!20 models

> fitmap #35.9 inMap #10

Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
W20_J4023_consensus_resampled.mrc (#10) using 930 atoms  
average map value = 0.2393, steps = 52  
shifted from previous position = 2.69  
rotated from previous position = 6.1 degrees  
atoms outside contour = 585, contour level = 0.259  
  
Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.98125869 0.10123862 -0.16395770 446.50000833  
0.05661840 -0.66183176 -0.74751126 606.96394850  
-0.18418942 -0.74278494 0.64369619 224.44341669  
Axis 0.09602403 0.41104534 -0.90654350  
Axis point 239.00882222 351.39277051 0.00000000  
Rotation angle (degrees) 178.58980379  
Shift along axis 88.89671334  
  

> fitmap #35.11 inMap #10

Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
W20_J4023_consensus_resampled.mrc (#10) using 1064 atoms  
average map value = 0.2705, steps = 48  
shifted from previous position = 1.17  
rotated from previous position = 3.69 degrees  
atoms outside contour = 361, contour level = 0.259  
  
Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.95447536 0.16472623 -0.24868064 445.72556094  
0.09748552 -0.61564640 -0.78196936 592.79673482  
-0.28191020 -0.77061325 0.57156090 289.62220826  
Axis 0.14970170 0.43804800 -0.88639909  
Axis point 253.33667423 363.30405703 0.00000000  
Rotation angle (degrees) 177.82629912  
Shift along axis 69.67843860  
  

> fitmap #39.1 inMap #10

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms  
average map value = 0.197, steps = 180  
shifted from previous position = 18.8  
rotated from previous position = 39.4 degrees  
atoms outside contour = 2326, contour level = 0.259  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77937618 0.53787625 -0.32134390 138.00151844  
0.38455520 -0.81555599 -0.43241846 137.27793171  
-0.49466156 0.21344218 -0.84246803 102.09006947  
Axis 0.94140147 0.25262649 -0.22347958  
Axis point 0.00000000 37.55487421 76.95697173  
Rotation angle (degrees) 159.93832539  
Shift along axis 141.77982886  
  

> select add #39.1

2567 atoms, 2609 bonds, 330 residues, 1 model selected  

> view matrix models
> #39.1,0.77938,0.53788,-0.32134,133.03,0.38456,-0.81556,-0.43242,136.21,-0.49466,0.21344,-0.84247,87.787

> fitmap #39.1 inMap #10

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms  
average map value = 0.197, steps = 148  
shifted from previous position = 15.2  
rotated from previous position = 0.0116 degrees  
atoms outside contour = 2326, contour level = 0.259  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77933517 0.53786894 -0.32145559 138.00257192  
0.38460571 -0.81561140 -0.43226900 137.27863469  
-0.49468691 0.21324878 -0.84250212 102.09071968  
Axis 0.94139228 0.25263228 -0.22351177  
Axis point 0.00000000 37.56089500 76.95480112  
Rotation angle (degrees) 159.94922815  
Shift along axis 141.77709241  
  

> view matrix models
> #39.1,0.77934,0.53787,-0.32146,130.24,0.38461,-0.81561,-0.43227,141.73,-0.49469,0.21325,-0.8425,88.079

> view matrix models
> #39.1,0.77934,0.53787,-0.32146,135.31,0.38461,-0.81561,-0.43227,140.11,-0.49469,0.21325,-0.8425,84.463

> fitmap #39.1 inMap #10

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms  
average map value = 0.197, steps = 172  
shifted from previous position = 18.1  
rotated from previous position = 0.0154 degrees  
atoms outside contour = 2326, contour level = 0.259  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77924517 0.53791820 -0.32159133 138.00026966  
0.38472109 -0.81564702 -0.43209909 137.28065889  
-0.49473897 0.21298817 -0.84253747 102.08755822  
Axis 0.94137014 0.25267283 -0.22355918  
Axis point 0.00000000 37.56685145 76.95023483  
Rotation angle (degrees) 159.96268257  
Shift along axis 141.77381369  
  

> view matrix models
> #39.1,0.77925,0.53792,-0.32159,128.09,0.38472,-0.81565,-0.4321,135.26,-0.49474,0.21299,-0.84254,82.235

> view matrix models
> #39.1,0.77925,0.53792,-0.32159,135.47,0.38472,-0.81565,-0.4321,136.17,-0.49474,0.21299,-0.84254,76.831

> view matrix models
> #39.1,0.77925,0.53792,-0.32159,139.06,0.38472,-0.81565,-0.4321,133.92,-0.49474,0.21299,-0.84254,83.878

> view matrix models
> #39.1,0.77925,0.53792,-0.32159,133.59,0.38472,-0.81565,-0.4321,136.36,-0.49474,0.21299,-0.84254,86.161

> view matrix models
> #39.1,0.77925,0.53792,-0.32159,137.64,0.38472,-0.81565,-0.4321,140.68,-0.49474,0.21299,-0.84254,88.092

> ui mousemode right "rotate selected models"

> view matrix models
> #39.1,0.88557,0.46445,-0.0069167,134.98,0.45496,-0.87029,-0.18867,138.57,-0.093649,0.16394,-0.98202,91.009

> fitmap #39.1 inMap #10

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms  
average map value = 0.197, steps = 144  
shifted from previous position = 19.4  
rotated from previous position = 24.7 degrees  
atoms outside contour = 2327, contour level = 0.259  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77925174 0.53807988 -0.32130481 137.99460111  
0.38488292 -0.81549555 -0.43224086 137.29386764  
-0.49460275 0.21315971 -0.84257407 102.10795439  
Axis 0.94137004 0.25276936 -0.22345043  
Axis point 0.00000000 37.55980635 76.95624722  
Rotation angle (degrees) 159.95253140  
Shift along axis 141.79160050  
  

> view matrix models
> #39.1,0.68606,0.65344,-0.3199,137.9,0.57062,-0.75605,-0.32059,137.24,-0.45135,0.037399,-0.89156,102.26

> ui mousemode right "translate selected models"

> view matrix models
> #39.1,0.68606,0.65344,-0.3199,131.56,0.57062,-0.75605,-0.32059,145.97,-0.45135,0.037399,-0.89156,83.123

> view matrix models
> #39.1,0.68606,0.65344,-0.3199,134.43,0.57062,-0.75605,-0.32059,139.6,-0.45135,0.037399,-0.89156,83.125

> view matrix models
> #39.1,0.68606,0.65344,-0.3199,130.69,0.57062,-0.75605,-0.32059,139.63,-0.45135,0.037399,-0.89156,81.892

> view matrix models
> #39.1,0.68606,0.65344,-0.3199,132.35,0.57062,-0.75605,-0.32059,136.91,-0.45135,0.037399,-0.89156,85.265

> view matrix models
> #39.1,0.68606,0.65344,-0.3199,127.51,0.57062,-0.75605,-0.32059,139.3,-0.45135,0.037399,-0.89156,87.993

> view matrix models
> #39.1,0.68606,0.65344,-0.3199,131.61,0.57062,-0.75605,-0.32059,143.53,-0.45135,0.037399,-0.89156,89.59

> fitmap #39.1 inMap #10

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J4023_consensus_resampled.mrc (#10) using 2567 atoms  
average map value = 0.197, steps = 144  
shifted from previous position = 14.5  
rotated from previous position = 13.3 degrees  
atoms outside contour = 2327, contour level = 0.259  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77919349 0.53804611 -0.32150254 137.99342007  
0.38489409 -0.81557949 -0.43207249 137.29343954  
-0.49468580 0.21292364 -0.84258500 102.10246297  
Axis 0.94135648 0.25275684 -0.22352173  
Axis point 0.00000000 37.56820104 76.95313719  
Rotation angle (degrees) 159.96533135  
Shift along axis 141.78073688  
  

> select subtract #39.1

Nothing selected  

> hide #39.1 models

> show #!33 models

> hide #33.1 models

> hide #33.2 models

> hide #33.3 models

> hide #!33.4 models

> hide #33.5 models

> hide #33.6 models

> hide #33.7 models

> hide #33.8 models

> hide #33.9 models

> hide #33.10 models

> hide #33.11 models

> hide #33.12 models

> fitmap #33.13 inMap #10

Fit molecule COPI_cyto_J4028_model M (#33.13) to map
W20_J4023_consensus_resampled.mrc (#10) using 4552 atoms  
average map value = 0.2144, steps = 128  
shifted from previous position = 5.65  
rotated from previous position = 7.59 degrees  
atoms outside contour = 3456, contour level = 0.259  
  
Position of COPI_cyto_J4028_model M (#33.13) relative to
W20_J4023_consensus_resampled.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.35039846 -0.93657228 -0.00730075 262.48644706  
-0.86127456 0.31914510 0.39541441 178.27483489  
-0.36800418 0.14484055 -0.91847382 254.98975169  
Axis -0.56232261 0.80946867 0.16897857  
Axis point 210.46623440 0.00000000 89.03589265  
Rotation angle (degrees) 167.12630425  
Shift along axis 39.79363149  
  

> hide #!20 models

> hide #!35.11 models

> show #!35.11 models

> hide #!35.11 models

> hide #35.9 models

> show #35.9 models

> hide #33.13 models

> hide #35.9 models

> show #33.13 models

> ui mousemode right select

Drag select of 242 residues  

> select up

2060 atoms, 2089 bonds, 262 residues, 1 model selected  

> select clear

Drag select of 128 residues  

> select up

1192 atoms, 1211 bonds, 151 residues, 1 model selected  

> delete sel

> select clear

Drag select of 5 residues  
Drag select of 16 residues  
Drag select of 64 residues, 1 pseudobonds  

> select up

587 atoms, 592 bonds, 1 pseudobond, 73 residues, 2 models selected  

> delete sel

Drag select of 4 residues, 1 pseudobonds  

> delete sel

Drag select of 1 pseudobonds  

> delete sel

> select add #33.13

2744 atoms, 2786 bonds, 1 pseudobond, 354 residues, 2 models selected  

> select subtract #33.13

Nothing selected  

> combine #30.13

> hide #!33.13 models

Drag select of 172 residues  

> select up

1391 atoms, 1413 bonds, 176 residues, 1 model selected  

> delete sel

Drag select of 24 residues  

> select up

388 atoms, 392 bonds, 48 residues, 1 model selected  

> delete sel

Drag select of 15 residues, 1 pseudobonds  

> select up

269 atoms, 268 bonds, 1 pseudobond, 37 residues, 2 models selected  

> select clear

Drag select of 9 residues, 1 pseudobonds  

> select up

155 atoms, 154 bonds, 1 pseudobond, 21 residues, 2 models selected  

> delete sel

Drag select of 7 residues  

> select up

136 atoms, 136 bonds, 19 residues, 1 model selected  

> select clear

> fitmap #42 inMap #20

Fit molecule copy of COPI_cyto_J4025_model M (#42) to map
W20_J4028_consensus_resampled.mrc (#20) using 2618 atoms  
average map value = 0.306, steps = 180  
shifted from previous position = 23.6  
rotated from previous position = 33.1 degrees  
atoms outside contour = 931, contour level = 0.25474  
  
Position of copy of COPI_cyto_J4025_model M (#42) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.14963361 -0.97522083 0.16295437 216.33302484  
-0.96633931 0.17912766 0.18466631 233.37303521  
-0.20928006 -0.12983692 -0.96919773 254.43371461  
Axis -0.64527959 0.76372913 0.01822260  
Axis point 227.29901935 0.00000000 104.64971477  
Rotation angle (degrees) 165.89525591  
Shift along axis 43.27494515  
  

> show #!20 models

> show #35.9 models

> hide #35.9 models

> show #35.9 models

> fitmap #35.9 inMap #20

Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
W20_J4028_consensus_resampled.mrc (#20) using 930 atoms  
average map value = 0.3762, steps = 56  
shifted from previous position = 2.58  
rotated from previous position = 5.97 degrees  
atoms outside contour = 300, contour level = 0.25474  
  
Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.95707237 0.18100601 -0.22638311 433.92940718  
0.05310912 -0.65830260 -0.75087756 607.96749602  
-0.28494194 -0.73066717 0.62043016 258.74353581  
Axis 0.14221667 0.41206734 -0.89998607  
Axis point 248.77691524 354.86529873 0.00000000  
Rotation angle (degrees) 175.92541914  
Shift along axis 79.36996533  
  

> show #35.8 models

> hide #35.8 models

> show #!35.11 models

> fitmap #35.11 inMap #20

Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
W20_J4028_consensus_resampled.mrc (#20) using 1064 atoms  
average map value = 0.3378, steps = 88  
shifted from previous position = 0.716  
rotated from previous position = 7.18 degrees  
atoms outside contour = 284, contour level = 0.25474  
  
Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.94111577 0.21871586 -0.25780707 426.29452223  
0.03665885 -0.69203983 -0.72092788 614.47706636  
-0.33609112 -0.68792750 0.64327172 250.03704434  
Axis 0.16425992 0.38966017 -0.90619183  
Axis point 251.98330593 349.53072602 0.00000000  
Rotation angle (degrees) 174.23481815  
Shift along axis 82.87881842  
  

> hide #!20 models

> show #!20 models

> hide #!20 models

> select #35.9/L:331

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show #!20 models

> hide #!20 models

> delete sel

> select #35.9/L:332

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #35.9/L:333

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete sel

> select #35.9/L:334

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete sel

> select #35.9/L:335

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #35.9/L:336

6 atoms, 5 bonds, 1 residue, 1 model selected  

> delete sel

> select #35.9/L:337

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> fitmap #35.9 inMap #20

Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
W20_J4028_consensus_resampled.mrc (#20) using 878 atoms  
average map value = 0.3829, steps = 44  
shifted from previous position = 0.138  
rotated from previous position = 1.65 degrees  
atoms outside contour = 274, contour level = 0.25474  
  
Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
W20_J4028_consensus_resampled.mrc (#20) coordinates:  
Matrix rotation and translation  
-0.96329901 0.17783180 -0.20107426 427.85994614  
0.03340558 -0.66383109 -0.74713610 614.70583444  
-0.26634390 -0.72643247 0.63352726 246.72265827  
Axis 0.12953006 0.40835260 -0.90358736  
Axis point 244.47252749 353.86664751 0.00000000  
Rotation angle (degrees) 175.41613396  
Shift along axis 83.50197716  
  

> show #!20 models

> show #33.1 models

> show #33.2 models

> show #33.3 models

> show #!33.4 models

> show #33.5 models

> show #33.6 models

> show #33.7 models

> show #33.8 models

> show #33.9 models

> show #33.10 models

> show #33.11 models

> show #33.12 models

> combine #33.1 #33.2 #33.3 #33.4 #33.5 #33.6 #33.7 #33.8 #33.9 #33.10 #33.11
> #33.12 #41 #35.9 #35.11

Remapping chain ID 'A' in COPI_cyto_J4017_model #41 to 'P'  
Remapping chain ID 'B' in COPI_cyto_J4017_model #41 to 'Q'  
Remapping chain ID 'C' in COPI_cyto_J4017_model #41 to 'R'  
Remapping chain ID 'D' in COPI_cyto_J4017_model #41 to 'S'  
Remapping chain ID 'E' in COPI_cyto_J4017_model #41 to 'T'  
Remapping chain ID 'F' in COPI_cyto_J4017_model #41 to 'U'  
Remapping chain ID 'G' in COPI_cyto_J4017_model #41 to 'V'  
Remapping chain ID 'H' in COPI_cyto_J4017_model #41 to 'W'  
Remapping chain ID 'I' in COPI_cyto_J4017_model #41 to 'X'  
Remapping chain ID 'J' in COPI_cyto_J4017_model #41 to 'Y'  
Remapping chain ID 'K' in COPI_cyto_J4017_model #41 to 'Z'  
Remapping chain ID 'L' in COPI_cyto_J4017_model #41 to 'a'  
Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'b'  
Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'c'  

> rename #41 COPI_cyto_J4027_model

> rename #43 COPI_cyto_J4028_model

> hide #!20 models

> show #!22 models

> hide #!43 models

> show #!43 models

> hide #!22 models

> show #!20 models

> hide #!20 models

> hide #!43 models

> hide #!42 models

> hide #!33 models

> show #!16 models

> hide #35.9 models

> show #35.9 models

> hide #!35 models

> show #!40 models

> hide #!40 models

> hide #!16 models

> show #!18 models

> show #!41 models

> hide #!41 models

> show #!43 models

> hide #!18 models

> show #!20 models

> close #43

> show #!42 models

> show #!35 models

> show #!33 models

> combine #33.1 #33.2 #33.3 #33.4 #33.5 #33.6 #33.7 #33.8 #33.9 #33.10 #33.11
> #33.12 #42 #35.9 #35.11

Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N'  
Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O'  

> rename #43 COPI_cyto_J4028_model

> hide #!43 models

> show #!43 models

> hide #!42 models

> hide #!35 models

> hide #!33 models

> hide #!43 models

> show #!43 models

> hide #!43 models

> hide #!20 models

> show #!22 models

> show #!34 models

> hide #34.13 models

> show #!35 models

> show #39.1 models

> fitmap #35.9 inMap #22

Fit molecule COPI_soluble_job155_dhelix.pdb L (#35.9) to map
W20_J3988_consensus_resampled.mrc (#22) using 878 atoms  
average map value = 0.3662, steps = 64  
shifted from previous position = 1.16  
rotated from previous position = 1.8 degrees  
atoms outside contour = 302, contour level = 0.28583  
  
Position of COPI_soluble_job155_dhelix.pdb L (#35.9) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.95887497 0.16676765 -0.22966788 440.72789628  
0.05962226 -0.67277255 -0.73744307 605.37107525  
-0.27749589 -0.72080903 0.63516169 247.24016866  
Axis 0.14036124 0.40358181 -0.90411307  
Axis point 248.93620927 350.83028914 0.00000000  
Rotation angle (degrees) 176.60298227  
Shift along axis 82.64480207  
  

> fitmap #35.11 inMap #22

Fit molecule COPI_soluble_job155_dhelix.pdb N (#35.11) to map
W20_J3988_consensus_resampled.mrc (#22) using 1064 atoms  
average map value = 0.384, steps = 72  
shifted from previous position = 0.949  
rotated from previous position = 1.29 degrees  
atoms outside contour = 322, contour level = 0.28583  
  
Position of COPI_soluble_job155_dhelix.pdb N (#35.11) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.93994555 0.23565898 -0.24691539 415.54469230  
0.01481361 -0.69455698 -0.71928517 620.65417336  
-0.34100282 -0.67974661 0.64935478 246.72523257  
Axis 0.16251841 0.38673478 -0.90775767  
Axis point 249.64126104 349.36740731 0.00000000  
Rotation angle (degrees) 173.01304550  
Shift along axis 83.59549488  
  

> fitmap #39.1 inMap #22

Fit molecule fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1) to
map W20_J3988_consensus_resampled.mrc (#22) using 2567 atoms  
average map value = 0.2763, steps = 92  
shifted from previous position = 10.5  
rotated from previous position = 9.1 degrees  
atoms outside contour = 1395, contour level = 0.28583  
  
Position of fold_2025_01_17_alpha1_330gamma1_330zeta_model_0.cif A (#39.1)
relative to W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
0.78195191 0.59824553 -0.17508140 136.85372786  
0.46784009 -0.74887041 -0.46938125 138.09735041  
-0.41191852 0.28512347 -0.86546389 93.90913619  
Axis 0.94138597 0.29549867 -0.16270522  
Axis point 0.00000000 34.34868013 69.05412162  
Rotation angle (degrees) 156.37546309  
Shift along axis 154.36025614  
  

> fitmap #42 inMap #22

Fit molecule copy of COPI_cyto_J4025_model M (#42) to map
W20_J3988_consensus_resampled.mrc (#22) using 2618 atoms  
average map value = 0.3079, steps = 52  
shifted from previous position = 1.27  
rotated from previous position = 2.32 degrees  
atoms outside contour = 1148, contour level = 0.28583  
  
Position of copy of COPI_cyto_J4025_model M (#42) relative to
W20_J3988_consensus_resampled.mrc (#22) coordinates:  
Matrix rotation and translation  
-0.16260849 -0.97678601 0.13945458 220.44563836  
-0.95843463 0.18994779 0.21289181 227.66250748  
-0.23443883 -0.09904008 -0.96707265 255.16502900  
Axis -0.64015894 0.76731881 0.03766144  
Axis point 225.62353549 0.00000000 102.00127381  
Rotation angle (degrees) 165.89874346  
Shift along axis 43.17936097  
  

> hide #39.1 models

> show #!42 models

> combine #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 #34.9 #34.10 #34.11
> #34.12 #42 #35.9 #35.11

Remapping chain ID 'L' in COPI_soluble_job155_dhelix.pdb L #35.9 to 'N'  
Remapping chain ID 'N' in COPI_soluble_job155_dhelix.pdb N #35.11 to 'O'  

> rename #44 COPI_cyto_J3988_model

> hide #!42 models

> hide #!22 models

> show #!24 models

> hide #!44 models

> hide #!35 models

> hide #!24 models

> hide #!34 models

> show #!24 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!24 models

> show #!25 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!25 models

> show #!26 models

> hide #!26 models

> show #!27 models

> hide #!6 models

> show #!8 models

> hide #!27 models

> close #35

> close #36

> close #37-39

> close #42

> combine #24.1 #24.2 #24.3 #24.4 #24.5 #24.6 #24.7 #24.8 #24.9 #24.10 #24.11
> #24.12 #24.13

> hide #!8 models

> show #!1 models

> rename #35 COPI_cyto_J3623_model

> hide #!35 models

> show #!35 models

> combine #25.1 #25.2 #25.3 #25.4 #25.5 #25.6 #25.7 #25.8 #25.9 #25.10 #25.11
> #25.12 #25.13

> rename #36 COPI_cyto_J3987_model

> combine #26.1 #26.2 #26.3 #26.4 #26.5 #26.6 #26.7 #26.8 #26.9 #26.10 #26.11
> #26.12 #26.13

> rename #37 COPI_cyto_J4021_model

> combine #27.1 #27.2 #27.3 #27.4 #27.5 #27.6 #27.7 #27.8 #27.9 #27.10 #27.11
> #27.12 #27.13

> rename #38 COPI_cyto_J4022_model

> combine #28.1 #28.2 #28.3 #28.4 #28.5 #28.6 #28.7 #28.8 #28.9 #28.10 #28.11
> #28.12 #28.13

> rename #39 COPI_cyto_J4023_model

> combine #29.1 #29.2 #29.3 #29.4 #29.5 #29.6 #29.7 #29.8 #29.9 #29.10 #29.11
> #29.12 #29.13

> rename #42 COPI_cyto_J4024_model

> combine #30.1 #30.2 #30.3 #30.4 #30.5 #30.6 #30.7 #30.8 #30.9 #30.10 #30.11
> #30.12 #30.13

> hide #!42 models

> hide #!39 models

> hide #!38 models

> hide #!37 models

> hide #!36 models

> hide #!35 models

> rename #45 COPI_cyto_J4025_model

> save COPI_cyto_J3623_model.pdb #35

> save COPI_cyto_J3987_model.pdb #36

> save COPI_cyto_J4021_model.pdb #37

> save COPI_cyto_J4022_model.pdb #38

> save COPI_cyto_J4023_model.pdb #39

> save COPI_cyto_J4026_model.pdb #40

> save COPI_cyto_J4027_model.pdb #41

> save COPI_cyto_J4024_model.pdb #42

> save COPI_cyto_J4028_model.pdb #43

> save COPI_cyto_J3988_model.pdb #44

> save COPI_cyto_J4025_model.pdb #45

> hide #!45 models

> show #!5 models

> hide #!1 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!6 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!6 models

> show #!31 models

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/CombineFocusedMaps_33/composite_map.ccp4

Opened composite_map.ccp4 as #46, grid size 240,240,240, pixel 1.19, shown at
level 5.84, step 1, values float32  

> rename #46 composite_map_J4021_J4026.ccp4

> hide #!46 models

> show #!46 models

> hide #!6 models

> volume #46 level 4.356

> color #46 darkgrey models

> color #46 #a9a9a9c3 models

> color #46 #a9a9a9c0 models

> color #46 #a9a9a9bf models

> hide #!31 models

> show #!40 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

> hide #!46 models

> show #!46 models

> hide #!46 models

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J3987_ResolveCryoEM_34/J3987_denmod_map.ccp4

Opened J3987_denmod_map.ccp4 as #47, grid size 100,124,124, pixel 1.19, shown
at level 0.316, step 1, values float32  

> volume #47 level 0.168

> volume #47 level 0.08306

> close #47

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4021_ResolveCryoEM_35/J4021_denmod_map.ccp4

Opened J4021_denmod_map.ccp4 as #47, grid size 92,128,121, pixel 1.19, shown
at level 0.263, step 1, values float32  

> volume #47 level 0.1546

> volume #47 level 0.0986

> close #47

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4022_ResolveCryoEM_36/J4022_denmod_map.ccp4

Opened J4022_denmod_map.ccp4 as #47, grid size 92,126,116, pixel 1.19, shown
at level 0.256, step 1, values float32  

> volume #47 level 0.1136

> close #47

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4023_ResolveCryoEM_37/J4023_denmod_map.ccp4

Opened J4023_denmod_map.ccp4 as #47, grid size 92,125,117, pixel 1.19, shown
at level 0.26, step 1, values float32  

> volume #47 level 0.06747

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4024_ResolveCryoEM_38/J4024_denmod_map.ccp4

Opened J4024_denmod_map.ccp4 as #48, grid size 92,126,119, pixel 1.19, shown
at level 0.262, step 1, values float32  

> close #47

> volume #48 level 0.1111

> close #48

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4025_ResolveCryoEM_40/J4025_denmod_map.ccp4

Opened J4025_denmod_map.ccp4 as #47, grid size 91,128,120, pixel 1.19, shown
at level 0.235, step 1, values float32  

> volume #47 level 0.1354

> volume #47 level 0.09666

> close #47

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

——— End of log from Mon Jul 7 09:47:13 2025 ———

> view name session-start

opened ChimeraX session  

> show #!46 models

> open
> /Users/becca/Desktop/Postdoc/Phenix/W20_MM_cyto_COPI/J4021_J4027_CombineFocusedMaps_41/J4021_J4027_composite_map.ccp4

Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 5.81, step 1, values float32  

> color #47 darkgrey models

> color #47 #a9a9a9c1 models

> hide #!47 models

> hide #!46 models

> hide #!40 models

> show #!40 models

> hide #!40 models

> combine #40

> split #48 chains

Split copy of COPI_cyto_J4026_model (#48) into 15 models  
Chain information for copy of COPI_cyto_J4026_model A #48.1  
---  
Chain | Description  
A | No description available  
  
Chain information for copy of COPI_cyto_J4026_model B #48.2  
---  
Chain | Description  
B | No description available  
  
Chain information for copy of COPI_cyto_J4026_model C #48.3  
---  
Chain | Description  
C | No description available  
  
Chain information for copy of COPI_cyto_J4026_model D #48.4  
---  
Chain | Description  
D | No description available  
  
Chain information for copy of COPI_cyto_J4026_model E #48.5  
---  
Chain | Description  
E | No description available  
  
Chain information for copy of COPI_cyto_J4026_model F #48.6  
---  
Chain | Description  
F | No description available  
  
Chain information for copy of COPI_cyto_J4026_model G #48.7  
---  
Chain | Description  
G | No description available  
  
Chain information for copy of COPI_cyto_J4026_model H #48.8  
---  
Chain | Description  
H | No description available  
  
Chain information for copy of COPI_cyto_J4026_model I #48.9  
---  
Chain | Description  
I | No description available  
  
Chain information for copy of COPI_cyto_J4026_model J #48.10  
---  
Chain | Description  
J | No description available  
  
Chain information for copy of COPI_cyto_J4026_model K #48.11  
---  
Chain | Description  
K | No description available  
  
Chain information for copy of COPI_cyto_J4026_model L #48.12  
---  
Chain | Description  
L | No description available  
  
Chain information for copy of COPI_cyto_J4026_model M #48.13  
---  
Chain | Description  
M | No description available  
  
Chain information for copy of COPI_cyto_J4026_model N #48.14  
---  
Chain | Description  
N | No description available  
  
Chain information for copy of COPI_cyto_J4026_model O #48.15  
---  
Chain | Description  
O | No description available  
  

> show #!46 models

> fitmap #48.1 inMap #46

Fit molecule copy of COPI_cyto_J4026_model A (#48.1) to map
composite_map_J4021_J4026.ccp4 (#46) using 2590 atoms  
average map value = 8.012, steps = 44  
shifted from previous position = 0.024  
rotated from previous position = 0.0413 degrees  
atoms outside contour = 449, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model A (#48.1) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.42161671 -0.88866766 -0.18030295 281.35767523  
-0.78137178 0.25516130 0.56951811 159.89900138  
-0.46010598 0.38100198 -0.80196009 237.46670115  
Axis -0.53247943 0.79032688 0.30306613  
Axis point 207.11724288 0.00000000 70.73686916  
Rotation angle (degrees) 169.80392724  
Shift along axis 48.52341756  
  

> fitmap #48.2 inMap #46

Fit molecule copy of COPI_cyto_J4026_model B (#48.2) to map
composite_map_J4021_J4026.ccp4 (#46) using 2426 atoms  
average map value = 7.643, steps = 48  
shifted from previous position = 0.0352  
rotated from previous position = 0.149 degrees  
atoms outside contour = 405, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model B (#48.2) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.42061793 -0.88953902 -0.17832811 281.05427064  
-0.78226434 0.25604617 0.56789336 160.17141808  
-0.45950307 0.37836585 -0.80355226 237.63647217  
Axis -0.53290254 0.79059154 0.30162873  
Axis point 207.14962646 0.00000000 70.86650714  
Rotation angle (degrees) 169.75686245  
Shift along axis 48.53362146  
  

> fitmap #48.3 inMap #46

Fit molecule copy of COPI_cyto_J4026_model C (#48.3) to map
composite_map_J4021_J4026.ccp4 (#46) using 1612 atoms  
average map value = 6.339, steps = 64  
shifted from previous position = 0.137  
rotated from previous position = 1.31 degrees  
atoms outside contour = 282, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model C (#48.3) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.43767621 -0.88321497 -0.16843654 281.87335410  
-0.76783552 0.26967498 0.58112309 157.06406865  
-0.46783349 0.38367530 -0.79619414 237.77730124  
Axis -0.52408907 0.79469449 0.30625367  
Axis point 206.03117664 0.00000000 70.20592740  
Rotation angle (degrees) 169.14218802  
Shift along axis 49.91138003  
  

> fitmap #48.4 inMap #46

Fit molecule copy of COPI_cyto_J4026_model D (#48.4) to map
composite_map_J4021_J4026.ccp4 (#46) using 4745 atoms  
average map value = 6.217, steps = 64  
shifted from previous position = 0.346  
rotated from previous position = 0.851 degrees  
atoms outside contour = 894, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model D (#48.4) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.42924156 -0.88289723 -0.19037904 282.64245635  
-0.77884347 0.25509758 0.57299920 159.11506089  
-0.45733417 0.39423054 -0.79713722 235.42666761  
Axis -0.52934994 0.79047793 0.30811245  
Axis point 206.45398809 0.00000000 70.11358015  
Rotation angle (degrees) 170.27864285  
Shift along axis 48.69806493  
  

> fitmap #48.5 inMap #46

Fit molecule copy of COPI_cyto_J4026_model E (#48.5) to map
composite_map_J4021_J4026.ccp4 (#46) using 1876 atoms  
average map value = 6.728, steps = 28  
shifted from previous position = 0.0537  
rotated from previous position = 0.205 degrees  
atoms outside contour = 414, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model E (#48.5) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.41906414 -0.89016033 -0.17888502 280.98895035  
-0.78296435 0.25453348 0.56760863 160.29649800  
-0.45973045 0.37792501 -0.80362965 237.75201321  
Axis -0.53364295 0.79011139 0.30157785  
Axis point 207.27636606 0.00000000 70.89197237  
Rotation angle (degrees) 169.76271203  
Shift along axis 48.40505872  
  

> fitmap #48.6 inMap #46

Fit molecule copy of COPI_cyto_J4026_model F (#48.6) to map
composite_map_J4021_J4026.ccp4 (#46) using 2400 atoms  
average map value = 4.933, steps = 60  
shifted from previous position = 4.71  
rotated from previous position = 7.6 degrees  
atoms outside contour = 678, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model F (#48.6) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.53669929 -0.82504557 -0.17678715 281.80609510  
-0.72189432 0.34051286 0.60242808 144.12665157  
-0.43683232 0.45094436 -0.77834872 227.64701078  
Axis -0.47615916 0.81740061 0.32423556  
Axis point 193.11631392 -0.00000000 70.10143524  
Rotation angle (degrees) 170.84717448  
Shift along axis 57.43591697  
  

> fitmap #48.7 inMap #46

Fit molecule copy of COPI_cyto_J4026_model G (#48.7) to map
composite_map_J4021_J4026.ccp4 (#46) using 2302 atoms  
average map value = 5.406, steps = 80  
shifted from previous position = 4.73  
rotated from previous position = 4.21 degrees  
atoms outside contour = 580, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model G (#48.7) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.48330635 -0.85702087 -0.17869027 283.39251275  
-0.74444396 0.29492363 0.59901858 152.16224396  
-0.46067144 0.42253437 -0.78054247 232.42661347  
Axis -0.50253361 0.80293313 0.32055945  
Axis point 201.16168457 -0.00000000 68.72114991  
Rotation angle (degrees) 169.88674773  
Shift along axis 54.26839065  
  

> fitmap #48.8 inMap #46

Fit molecule copy of COPI_cyto_J4026_model H (#48.8) to map
composite_map_J4021_J4026.ccp4 (#46) using 420 atoms  
average map value = 7.082, steps = 56  
shifted from previous position = 3.46  
rotated from previous position = 2.58 degrees  
atoms outside contour = 93, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model H (#48.8) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.46181347 -0.87023765 -0.17150736 282.95432862  
-0.76161078 0.28994955 0.57955009 156.07549407  
-0.45461782 0.39826589 -0.79668497 236.09755101  
Axis -0.51312841 0.80134959 0.30747044  
Axis point 203.66513828 0.00000000 70.89396293  
Rotation angle (degrees) 169.82553836  
Shift along axis 52.47214622  
  

> fitmap #48.9 inMap #46

Fit molecule copy of COPI_cyto_J4026_model I (#48.9) to map
composite_map_J4021_J4026.ccp4 (#46) using 1573 atoms  
average map value = 5.892, steps = 72  
shifted from previous position = 1.08  
rotated from previous position = 2.82 degrees  
atoms outside contour = 307, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model I (#48.9) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.44042374 -0.87092293 -0.21799127 283.13278743  
-0.77489855 0.24614258 0.58219077 160.68330197  
-0.45338635 0.42533175 -0.78328394 232.61931758  
Axis -0.52509607 0.78800081 0.32144805  
Axis point 205.38082265 0.00000000 68.72443099  
Rotation angle (degrees) 171.41003245  
Shift along axis 52.72168395  
  

> fitmap #48.10 inMap #46

Fit molecule copy of COPI_cyto_J4026_model J (#48.10) to map
composite_map_J4021_J4026.ccp4 (#46) using 1112 atoms  
average map value = 6.367, steps = 68  
shifted from previous position = 0.853  
rotated from previous position = 2.18 degrees  
atoms outside contour = 324, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model J (#48.10) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.39606742 -0.89516479 -0.20447643 281.46766551  
-0.80125621 0.22817550 0.55310438 165.26116045  
-0.44846305 0.38290463 -0.80762922 236.59702773  
Axis -0.54558979 0.78211990 0.30103197  
Axis point 209.53544999 0.00000000 71.09106362  
Rotation angle (degrees) 171.02649245  
Shift along axis 46.91142523  
  

> fitmap #48.12 inMap #46

Fit molecule copy of COPI_cyto_J4026_model L (#48.12) to map
composite_map_J4021_J4026.ccp4 (#46) using 1420 atoms  
average map value = 6, steps = 48  
shifted from previous position = 0.00534  
rotated from previous position = 0.0308 degrees  
atoms outside contour = 490, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model L (#48.12) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.42201385 -0.88851995 -0.18010170 281.36850791  
-0.78123838 0.25562354 0.56949383 159.86937778  
-0.45996839 0.38103664 -0.80202255 237.46846236  
Axis -0.53229101 0.79047409 0.30301320  
Axis point 207.08142201 0.00000000 70.75583573  
Rotation angle (degrees) 169.80350204  
Shift along axis 48.55875296  
  

> fitmap #48.13 inMap #46

Fit molecule copy of COPI_cyto_J4026_model M (#48.13) to map
composite_map_J4021_J4026.ccp4 (#46) using 2567 atoms  
average map value = 6.934, steps = 48  
shifted from previous position = 0.0327  
rotated from previous position = 0.0247 degrees  
atoms outside contour = 577, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model M (#48.13) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.42198871 -0.88852999 -0.18011109 281.34034070  
-0.78150296 0.25580865 0.56904751 159.96958762  
-0.45954180 0.38088898 -0.80233717 237.44017007  
Axis -0.53232061 0.79053934 0.30279089  
Axis point 207.07606122 0.00000000 70.77828437  
Rotation angle (degrees) 169.82040522  
Shift along axis 48.59371022  
  

> fitmap #48.14 inMap #46

Fit molecule copy of COPI_cyto_J4026_model N (#48.14) to map
composite_map_J4021_J4026.ccp4 (#46) using 930 atoms  
average map value = 7.254, steps = 40  
shifted from previous position = 0.0472  
rotated from previous position = 0.247 degrees  
atoms outside contour = 214, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model N (#48.14) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.42294225 -0.88896586 -0.17566891 281.09587079  
-0.78004341 0.25851684 0.56982571 159.40297655  
-0.46114222 0.37803274 -0.80276965 237.94268675  
Axis -0.53164432 0.79132341 0.30192975  
Axis point 206.92420625 0.00000000 70.92756128  
Rotation angle (degrees) 169.60827201  
Shift along axis 48.53825925  
  

> fitmap #48.15 inMap #46

Fit molecule copy of COPI_cyto_J4026_model O (#48.15) to map
composite_map_J4021_J4026.ccp4 (#46) using 1064 atoms  
average map value = 6.216, steps = 60  
shifted from previous position = 0.0698  
rotated from previous position = 0.468 degrees  
atoms outside contour = 130, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4026_model O (#48.15) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.41919869 -0.88836490 -0.18729731 281.44552791  
-0.78315395 0.24946223 0.56959504 160.73613068  
-0.45928463 0.38545612 -0.80030071 236.81019199  
Axis -0.53389619 0.78860565 0.30505080  
Axis point 207.35794189 0.00000000 70.38133823  
Rotation angle (degrees) 170.06980434  
Shift along axis 48.73386479  
  

> color #48.13 gammav3

> color #48.14 gammav3

> color #48.15 gammav3

> combine #48.1 #48.2 #48.3 #48.4 #48.5 #48.6 #48.7 #48.8 #48.9 #48.10 #48.11
> #48.12 #48.13 #48.14 #48.15

> rename #49 Model_for_composite_J4021_J4026

> hide #!49 models

> hide #!46 models

> show #!47 models

> close #48

> combine #41

> split #48 chains

Split copy of COPI_cyto_J4027_model (#48) into 15 models  
Chain information for copy of COPI_cyto_J4027_model A #48.1  
---  
Chain | Description  
A | No description available  
  
Chain information for copy of COPI_cyto_J4027_model B #48.2  
---  
Chain | Description  
B | No description available  
  
Chain information for copy of COPI_cyto_J4027_model C #48.3  
---  
Chain | Description  
C | No description available  
  
Chain information for copy of COPI_cyto_J4027_model D #48.4  
---  
Chain | Description  
D | No description available  
  
Chain information for copy of COPI_cyto_J4027_model E #48.5  
---  
Chain | Description  
E | No description available  
  
Chain information for copy of COPI_cyto_J4027_model F #48.6  
---  
Chain | Description  
F | No description available  
  
Chain information for copy of COPI_cyto_J4027_model G #48.7  
---  
Chain | Description  
G | No description available  
  
Chain information for copy of COPI_cyto_J4027_model H #48.8  
---  
Chain | Description  
H | No description available  
  
Chain information for copy of COPI_cyto_J4027_model I #48.9  
---  
Chain | Description  
I | No description available  
  
Chain information for copy of COPI_cyto_J4027_model J #48.10  
---  
Chain | Description  
J | No description available  
  
Chain information for copy of COPI_cyto_J4027_model K #48.11  
---  
Chain | Description  
K | No description available  
  
Chain information for copy of COPI_cyto_J4027_model L #48.12  
---  
Chain | Description  
L | No description available  
  
Chain information for copy of COPI_cyto_J4027_model M #48.13  
---  
Chain | Description  
M | No description available  
  
Chain information for copy of COPI_cyto_J4027_model N #48.14  
---  
Chain | Description  
N | No description available  
  
Chain information for copy of COPI_cyto_J4027_model O #48.15  
---  
Chain | Description  
O | No description available  
  

> color #48.13 gammav3

> color #48.14 gammav3

> color #48.15 gammav3

> fitmap #48.15 inMap #46

Fit molecule copy of COPI_cyto_J4027_model O (#48.15) to map
composite_map_J4021_J4026.ccp4 (#46) using 1064 atoms  
average map value = 6.216, steps = 68  
shifted from previous position = 0.926  
rotated from previous position = 3.78 degrees  
atoms outside contour = 131, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4027_model O (#48.15) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.34404909 -0.93260747 -0.10896575 269.91254838  
-0.80984309 0.23600764 0.53707968 166.69850821  
-0.47516777 0.27302693 -0.83646393 251.15790315  
Axis -0.56437651 0.78270657 0.26239203  
Axis point 213.21055464 0.00000000 75.30227951  
Rotation angle (degrees) 166.47125621  
Shift along axis 44.04554723  
  

> fitmap #48.14 inMap #46

Fit molecule copy of COPI_cyto_J4027_model N (#48.14) to map
composite_map_J4021_J4026.ccp4 (#46) using 930 atoms  
average map value = 7.254, steps = 68  
shifted from previous position = 4.09  
rotated from previous position = 12.1 degrees  
atoms outside contour = 214, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4027_model N (#48.14) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.29521822 -0.95538003 0.00975828 254.00941556  
-0.83564878 0.26314499 0.48212638 171.86630354  
-0.46318175 0.13417799 -0.87604735 264.92556241  
Axis -0.58065970 0.78924699 0.19980868  
Axis point 215.16338827 0.00000000 83.71664964  
Rotation angle (degrees) 162.56553634  
Shift along axis 41.08635962  
  

> fitmap #48.13 inMap #46

Fit molecule copy of COPI_cyto_J4027_model M (#48.13) to map
composite_map_J4021_J4026.ccp4 (#46) using 2567 atoms  
average map value = 6.934, steps = 184  
shifted from previous position = 24.3  
rotated from previous position = 38.5 degrees  
atoms outside contour = 574, contour level = 4.3561  
  
Position of copy of COPI_cyto_J4027_model M (#48.13) relative to
composite_map_J4021_J4026.ccp4 (#46) coordinates:  
Matrix rotation and translation  
-0.06511231 -0.96101824 0.26870867 188.55069019  
-0.97216064 0.12183140 0.20015198 237.48407748  
-0.22508686 -0.24819563 -0.94219682 265.26082374  
Axis -0.67212131 0.74025262 -0.01670366  
Axis point 232.93504959 0.00000000 109.96611159  
Rotation angle (degrees) 160.51672010  
Shift along axis 44.63844706  
  

> fitmap #48.13 inMap #47

Fit molecule copy of COPI_cyto_J4027_model M (#48.13) to map
J4021_J4027_composite_map.ccp4 (#47) using 2567 atoms  
average map value = 5.305, steps = 140  
shifted from previous position = 20.1  
rotated from previous position = 23.5 degrees  
atoms outside contour = 1497, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model M (#48.13) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.20584357 -0.97794249 -0.03545317 247.21508377  
-0.89336671 0.17300799 0.41468563 196.10217944  
-0.39940501 0.11703305 -0.90927384 267.43384909  
Axis -0.62307640 0.76186070 0.17704255  
Axis point 224.46487691 0.00000000 89.15375612  
Rotation angle (degrees) 166.18089851  
Shift along axis 42.71583076  
  

> close #48

> combine #41

> split #48 chains

Split copy of COPI_cyto_J4027_model (#48) into 15 models  
Chain information for copy of COPI_cyto_J4027_model A #48.1  
---  
Chain | Description  
A | No description available  
  
Chain information for copy of COPI_cyto_J4027_model B #48.2  
---  
Chain | Description  
B | No description available  
  
Chain information for copy of COPI_cyto_J4027_model C #48.3  
---  
Chain | Description  
C | No description available  
  
Chain information for copy of COPI_cyto_J4027_model D #48.4  
---  
Chain | Description  
D | No description available  
  
Chain information for copy of COPI_cyto_J4027_model E #48.5  
---  
Chain | Description  
E | No description available  
  
Chain information for copy of COPI_cyto_J4027_model F #48.6  
---  
Chain | Description  
F | No description available  
  
Chain information for copy of COPI_cyto_J4027_model G #48.7  
---  
Chain | Description  
G | No description available  
  
Chain information for copy of COPI_cyto_J4027_model H #48.8  
---  
Chain | Description  
H | No description available  
  
Chain information for copy of COPI_cyto_J4027_model I #48.9  
---  
Chain | Description  
I | No description available  
  
Chain information for copy of COPI_cyto_J4027_model J #48.10  
---  
Chain | Description  
J | No description available  
  
Chain information for copy of COPI_cyto_J4027_model K #48.11  
---  
Chain | Description  
K | No description available  
  
Chain information for copy of COPI_cyto_J4027_model L #48.12  
---  
Chain | Description  
L | No description available  
  
Chain information for copy of COPI_cyto_J4027_model M #48.13  
---  
Chain | Description  
M | No description available  
  
Chain information for copy of COPI_cyto_J4027_model N #48.14  
---  
Chain | Description  
N | No description available  
  
Chain information for copy of COPI_cyto_J4027_model O #48.15  
---  
Chain | Description  
O | No description available  
  

> color #48.13 gammav3

> color #48.14 gammav3

> color #48.15 gammav3

> fitmap #48.15 inMap #47

Fit molecule copy of COPI_cyto_J4027_model O (#48.15) to map
J4021_J4027_composite_map.ccp4 (#47) using 1064 atoms  
average map value = 7.175, steps = 80  
shifted from previous position = 0.0377  
rotated from previous position = 0.0512 degrees  
atoms outside contour = 362, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model O (#48.15) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36445970 -0.91742956 -0.15966261 274.93147533  
-0.79741803 0.21892271 0.56231428 164.22520611  
-0.48092997 0.33225874 -0.81136337 243.41623113  
Axis -0.55708089 0.77795083 0.29060864  
Axis point 211.70950704 0.00000000 70.89847596  
Rotation angle (degrees) 168.08366956  
Shift along axis 45.33892553  
  

> fitmap #48.14 inMap #47

Fit molecule copy of COPI_cyto_J4027_model N (#48.14) to map
J4021_J4027_composite_map.ccp4 (#47) using 930 atoms  
average map value = 7.843, steps = 48  
shifted from previous position = 0.0452  
rotated from previous position = 0.236 degrees  
atoms outside contour = 308, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model N (#48.14) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36749036 -0.91663154 -0.15728153 275.08372435  
-0.79611294 0.22261900 0.56271217 163.59058237  
-0.48078586 0.33200516 -0.81155255 243.40917516  
Axis -0.55562941 0.77912031 0.29025419  
Axis point 211.38295724 0.00000000 71.01177343  
Rotation angle (degrees) 168.01774651  
Shift along axis 45.26267005  
  

> fitmap #48.13 inMap #47

Fit molecule copy of COPI_cyto_J4027_model M (#48.13) to map
J4021_J4027_composite_map.ccp4 (#47) using 2567 atoms  
average map value = 6.181, steps = 48  
shifted from previous position = 0.0646  
rotated from previous position = 0.137 degrees  
atoms outside contour = 1105, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model M (#48.13) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36546244 -0.91673285 -0.16136328 275.21816301  
-0.79822949 0.21948305 0.56094285 164.44314904  
-0.47881823 0.33380847 -0.81197600 242.98792253  
Axis -0.55679103 0.77820041 0.29049589  
Axis point 211.65663706 0.00000000 70.90505517  
Rotation angle (degrees) 168.23094482  
Shift along axis 45.31771373  
  

> fitmap #48.12 inMap #47

Fit molecule copy of COPI_cyto_J4027_model L (#48.12) to map
J4021_J4027_composite_map.ccp4 (#47) using 1420 atoms  
average map value = 5.269, steps = 64  
shifted from previous position = 0.0436  
rotated from previous position = 0.124 degrees  
atoms outside contour = 716, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model L (#48.12) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36575950 -0.91679867 -0.16031284 275.10067764  
-0.79603501 0.21891045 0.56427520 163.73853261  
-0.48223259 0.33400364 -0.80987241 243.20437721  
Axis -0.55646287 0.77793538 0.29183150  
Axis point 211.57205619 0.00000000 70.70465662  
Rotation angle (degrees) 168.05887425  
Shift along axis 45.26938091  
  

> fitmap #48.11 inMap #47

Fit molecule copy of COPI_cyto_J4027_model K (#48.11) to map
J4021_J4027_composite_map.ccp4 (#47) using 319 atoms  
average map value = 6.544, steps = 680  
shifted from previous position = 34.4  
rotated from previous position = 55.2 degrees  
atoms outside contour = 122, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model K (#48.11) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
0.24248330 -0.95058432 0.19388478 218.57357673  
-0.33056267 0.10693534 0.93770633 73.53913137  
-0.91210207 -0.29146919 -0.28829766 267.39969287  
Axis -0.69605025 0.62629170 0.35110220  
Axis point 0.00000000 252.37218567 153.78684989  
Rotation angle (degrees) 117.99791989  
Shift along axis -12.19662658  
  

> ui tool show Matchmaker

> matchmaker #48.11 to #49

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Model_for_composite_J4021_J4026, chain K (#49) with copy of
COPI_cyto_J4027_model K, chain K (#48.11), sequence alignment score = 192.1  
RMSD between 37 pruned atom pairs is 0.000 angstroms; (across all 37 pairs:
0.000)  
  

> fitmap #48.10 inMap #47

Fit molecule copy of COPI_cyto_J4027_model J (#48.10) to map
J4021_J4027_composite_map.ccp4 (#47) using 1112 atoms  
average map value = 6.595, steps = 68  
shifted from previous position = 0.392  
rotated from previous position = 3.79 degrees  
atoms outside contour = 449, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model J (#48.10) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36954265 -0.92395010 -0.09876469 269.14351053  
-0.79489549 0.25928902 0.54855298 162.57033903  
-0.48122698 0.28122133 -0.83026211 249.17503135  
Axis -0.55216997 0.78997075 0.26656057  
Axis point 209.80677258 0.00000000 74.24424921  
Rotation angle (degrees) 165.99103601  
Shift along axis 46.23308621  
  

> fitmap #48.9 inMap #47

Fit molecule copy of COPI_cyto_J4027_model I (#48.9) to map
J4021_J4027_composite_map.ccp4 (#47) using 1573 atoms  
average map value = 5.861, steps = 68  
shifted from previous position = 1.24  
rotated from previous position = 3.45 degrees  
atoms outside contour = 773, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model I (#48.9) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.37973756 -0.89954761 -0.21590159 277.24792433  
-0.80457095 0.20595800 0.55699812 167.23271540  
-0.45657967 0.38522125 -0.80195986 236.87971276  
Axis -0.55310174 0.77495569 0.30581391  
Axis point 209.49101626 0.00000000 70.11224809  
Rotation angle (degrees) 171.06667095  
Shift along axis 48.69274569  
  

> fitmap #48.8 inMap #47

Fit molecule copy of COPI_cyto_J4027_model H (#48.8) to map
J4021_J4027_composite_map.ccp4 (#47) using 420 atoms  
average map value = 6.824, steps = 56  
shifted from previous position = 3.38  
rotated from previous position = 2.53 degrees  
atoms outside contour = 149, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model H (#48.8) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.40542761 -0.90093167 -0.15475978 276.94991852  
-0.78307394 0.25494593 0.56727223 160.97102962  
-0.47161814 0.35117617 -0.80885823 241.79873195  
Axis -0.53858123 0.78971345 0.29373956  
Axis point 207.95662584 0.00000000 71.49993787  
Rotation angle (degrees) 168.42701468  
Shift along axis 48.98681208  
  

> fitmap #48.7 inMap #47

Fit molecule copy of COPI_cyto_J4027_model G (#48.7) to map
J4021_J4027_composite_map.ccp4 (#47) using 2302 atoms  
average map value = 5.298, steps = 64  
shifted from previous position = 4.62  
rotated from previous position = 4.04 degrees  
atoms outside contour = 1402, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model G (#48.7) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.42560093 -0.89008522 -0.16313234 277.69917989  
-0.76548490 0.25798571 0.58947118 157.21311144  
-0.48259377 0.37575482 -0.79114574 238.50649670  
Axis -0.52893684 0.79065037 0.30837932  
Axis point 205.81643686 0.00000000 68.93017279  
Rotation angle (degrees) 168.34463133  
Shift along axis 50.96574868  
  

> fitmap #48.6 inMap #47

Fit molecule copy of COPI_cyto_J4027_model F (#48.6) to map
J4021_J4027_composite_map.ccp4 (#47) using 2400 atoms  
average map value = 4.862, steps = 56  
shifted from previous position = 4.53  
rotated from previous position = 7.12 degrees  
atoms outside contour = 1891, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model F (#48.6) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.47631791 -0.86443647 -0.16084418 276.54476513  
-0.74836077 0.30252539 0.59028346 150.15879842  
-0.46160309 0.40153206 -0.79100860 234.60647851  
Axis -0.50526012 0.80508798 0.31071780  
Axis point 198.13646970 0.00000000 70.54602612  
Rotation angle (degrees) 169.23470102  
Shift along axis 54.06041328  
  

> fitmap #48.5 inMap #47

Fit molecule copy of COPI_cyto_J4027_model E (#48.5) to map
J4021_J4027_composite_map.ccp4 (#47) using 1876 atoms  
average map value = 6.882, steps = 40  
shifted from previous position = 0.0401  
rotated from previous position = 0.0808 degrees  
atoms outside contour = 679, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model E (#48.5) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36460635 -0.91721639 -0.16055006 274.96464339  
-0.79803633 0.21895894 0.56142232 164.31313284  
-0.47979187 0.33282292 -0.81180581 243.25738221  
Axis -0.55710084 0.77799805 0.29044395  
Axis point 211.64530256 0.00000000 70.95305334  
Rotation angle (degrees) 168.16062068  
Shift along axis 45.30489541  
  

> fitmap #48.4 inMap #47

Fit molecule copy of COPI_cyto_J4027_model D (#48.4) to map
J4021_J4027_composite_map.ccp4 (#47) using 4745 atoms  
average map value = 6.326, steps = 80  
shifted from previous position = 0.232  
rotated from previous position = 0.637 degrees  
atoms outside contour = 1901, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model D (#48.4) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36403643 -0.91927407 -0.14970864 274.32296003  
-0.79661223 0.22402751 0.56144514 163.63243958  
-0.48258310 0.32364622 -0.81385913 244.76587458  
Axis -0.55679826 0.77941446 0.28720862  
Axis point 211.67256763 0.00000000 71.48567291  
Rotation angle (degrees) 167.67003358  
Shift along axis 45.09381034  
  

> fitmap #48.3 inMap #47

Fit molecule copy of COPI_cyto_J4027_model C (#48.3) to map
J4021_J4027_composite_map.ccp4 (#47) using 1612 atoms  
average map value = 6.318, steps = 80  
shifted from previous position = 0.228  
rotated from previous position = 1.41 degrees  
atoms outside contour = 653, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model C (#48.3) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.38173446 -0.91224090 -0.14864510 275.71683603  
-0.78322797 0.23388065 0.57606754 161.04568217  
-0.49074715 0.33632783 -0.80377288 243.57494299  
Axis -0.54833896 0.78246479 0.29508175  
Axis point 210.53404344 0.00000000 70.11714477  
Rotation angle (degrees) 167.37286555  
Shift along axis 46.70081412  
  

> fitmap #48.2 inMap #47

Fit molecule copy of COPI_cyto_J4027_model B (#48.2) to map
J4021_J4027_composite_map.ccp4 (#47) using 2426 atoms  
average map value = 7.483, steps = 48  
shifted from previous position = 0.0329  
rotated from previous position = 0.105 degrees  
atoms outside contour = 734, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model B (#48.2) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36430973 -0.91755945 -0.15925792 274.83521303  
-0.79785551 0.21931761 0.56153930 164.30315268  
-0.48031762 0.33163904 -0.81197940 243.32909311  
Axis -0.55716005 0.77808367 0.29010081  
Axis point 211.66844489 0.00000000 70.92695219  
Rotation angle (degrees) 168.09354740  
Shift along axis 45.30436790  
  

> fitmap #48.1 inMap #47

Fit molecule copy of COPI_cyto_J4027_model A (#48.1) to map
J4021_J4027_composite_map.ccp4 (#47) using 2590 atoms  
average map value = 7.767, steps = 64  
shifted from previous position = 0.0157  
rotated from previous position = 0.0377 degrees  
atoms outside contour = 732, contour level = 5.8074  
  
Position of copy of COPI_cyto_J4027_model A (#48.1) relative to
J4021_J4027_composite_map.ccp4 (#47) coordinates:  
Matrix rotation and translation  
-0.36433385 -0.91729312 -0.16073020 274.99544480  
-0.79752965 0.21821532 0.56243093 164.22320875  
-0.48084022 0.33309973 -0.81107168 243.29313210  
Axis -0.55718331 0.77773961 0.29097743  
Axis point 211.71070241 0.00000000 70.85027180  
Rotation angle (degrees) 168.12395214  
Shift along axis 45.29283319  
  

> combine #48.1 #48.2 #48.3 #48.4 #48.5 #48.6 #48.7 #48.8 #48.9 #48.10 #48.11
> #48.12 #48.13 #48.14 #48.15

> rename #50 Model_for_composite_J4021_J4027

> close #48

> show #!49 models

> hide #!49 models

> hide #!50 models

> save composite_model_J4021_J4026.pdb #49

> save composite_model_J4021_J4027.pdb #50

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

> hide #!47 models

> show #!1 models

> color #1 #a9a9a9bf models

> ui tool show "Surface Color"

> ui tool show "Color Zone"

> color zone #1 near #35 distance 6

> hide #!1 models

> show #!1 models

> select #35/K

319 atoms, 320 bonds, 37 residues, 1 model selected  

> hide #!1 models

> show #!35 models

> select #35/M

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #35

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected  

> hide #!35 models

> select subtract #35

Nothing selected  

> show #!36 models

> hide #!36 models

> show #!37 models

> select #36/M

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select #37/M

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #37

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected  

> select subtract #37

Nothing selected  

> hide #!37 models

> show #!38 models

> select #38/M

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select #39/m

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #39

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected  

> select subtract #39

Nothing selected  

> hide #!38 models

> show #!39 models

> hide #!39 models

> show #!40 models

> select #40/m

2567 atoms, 2609 bonds, 330 residues, 1 model selected  

> color sel gammav3

> select #40/n

930 atoms, 941 bonds, 118 residues, 1 model selected  

> color sel gammav3

> select #40/o

1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected  

> color sel gammav3

> select #41/m

2567 atoms, 2609 bonds, 330 residues, 1 model selected  

> hide #!40 models

> show #!41 models

> color sel gammav3

> select #41/n

930 atoms, 941 bonds, 118 residues, 1 model selected  

> color sel gammav3

> select #41/o

1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected  

> color sel gammav3

> select add #41

27356 atoms, 27866 bonds, 2 pseudobonds, 3436 residues, 2 models selected  

> select subtract #41

Nothing selected  

> hide #!41 models

> show #!42 models

> select #42/m

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #42

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected  

> select subtract #42

Nothing selected  

> hide #!42 models

> show #!43 models

> select #43/m

2618 atoms, 2660 bonds, 337 residues, 1 model selected  

> color sel gammav3

> select #43/n

878 atoms, 889 bonds, 111 residues, 1 model selected  

> color sel gammav3

> select #43/o

1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected  

> color sel gammav3

> select add #43

27355 atoms, 27865 bonds, 2 pseudobonds, 3436 residues, 2 models selected  

> hide #!43 models

> select subtract #43

Nothing selected  

> show #!44 models

> select #44/o

1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected  

> color sel gammav3

> select #44/n

878 atoms, 889 bonds, 111 residues, 1 model selected  

> color sel gammav3

> select #44/m

2618 atoms, 2660 bonds, 337 residues, 1 model selected  

> color sel gammav3

> select add #44

27355 atoms, 27865 bonds, 2 pseudobonds, 3436 residues, 2 models selected  

> hide #!44 models

> select subtract #44

Nothing selected  

> show #!45 models

> select #45/m

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #45

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected  

> select subtract #45

Nothing selected  

> hide #!45 models

> show #!1 models

> color zone #1 near #35 distance 6

> volume #1 level 0.1319

> color zone #1 near #35 distance 6.1

> color zone #1 near #35 distance 6.2

> color zone #1 near #35 distance 6.3

> color zone #1 near #35 distance 6.4

> color zone #1 near #35 distance 6.5

> color zone #1 near #35 distance 6.6

> color zone #1 near #35 distance 6.7

> color zone #1 near #35 distance 9

[Repeated 1 time(s)]

> volume #1 level 0.1857

> view view1

Expected an objects specifier or a view name or a keyword  

> view name view1

> rotate 90

Unknown command: rotate 90  

> turn 90

Expected an axis vector or a keyword  

> turn x 90

[Repeated 3 time(s)]

> turn y 90

[Repeated 3 time(s)]

> turn y -90

> view name view2

> turn y 90

> view view2

> turn y 180

> view name view3

> view view3

> turn y 180

> view name view4

[Repeated 1 time(s)]

> view view3

> view name view3

> view name view5

> lighting soft

> set silhouetteWidth 1.5

> ui tool show "Side View"

> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view5.png
> width 823 height 607 supersample 3 transparentBackground true

> view view3

> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view3.png
> width 823 height 607 supersample 3 transparentBackground true

> view view4

> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view4.png
> width 823 height 607 supersample 3 transparentBackground true

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4479_map_locres_J3623.mrc"

Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  

> ui tool show "Surface Color"

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #48 palette 2,#ff0000:4,#ffffff:10,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #48 palette 3,#ff0000:4,#ffffff:10,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #48 palette 4,#ff0000:6,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color single #1.1

> key red-white-blue :4 :6 :8 showTool true

> ui mousemode right "color key"

> color sample #1.1 map #48 palette 2.5,#ff0000:6,#ffffff:8,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> key red-white-blue :2.5 :6.0 :8.0 showTool true

> color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:8,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> key red-white-blue :2.5 :4.0 :8.0 showTool true

> color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:6.5,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> key red-white-blue :2.5 :4.0 :6.5 showTool true

> color single #1.1

> color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:6.5,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #48 palette 3,#ff0000:4,#ffffff:6.5,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> key red-white-blue :3.0 :4.0 :6.5 showTool true

> color sample #1.1 map #48 palette 3,#ff0000:4.5,#ffffff:6.5,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> key red-white-blue :3.0 :4.5 :6.5 showTool true

> color sample #1.1 map #48 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> key red-white-blue :3.0 :4.5 :6.0 showTool true

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4480_map_locres_J3623_v2.mrc"

Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4481_map_locres_J3623_v3.mrc"

Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32  

> hide #!52 models

> hide #!53 models

> color sample #1.1 map #52 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color single #1.1

> color sample #1.1 map #52 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color single #1.1

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:8,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color single #1.1

> color sample #1.1 map #53 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> color sample #1.1 map #53 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766  

> volume #1 level 0.1937

> view view5

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"

——— End of log from Mon Jul 7 17:31:35 2025 ———

> view name session-start

opened ChimeraX session  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments.cxs"

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2586_007_volume_map.mrc"

Opened cryosparc_P126_J2586_007_volume_map.mrc as #54, grid size 300,300,300,
pixel 1.24, shown at level 0.227, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J4482_map_locres.mrc"

Opened cryosparc_P126_J4482_map_locres.mrc as #55, grid size 400,400,400,
pixel 1.24, shown at level 39.3, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2954_map_locres_v3.mrc"

Opened cryosparc_P126_J2954_map_locres_v3.mrc as #56, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2953_map_locres_v2.mrc"

Opened cryosparc_P126_J2953_map_locres_v2.mrc as #57, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2952_map_locres_J2634_v1.mrc"

Opened cryosparc_P126_J2952_map_locres_J2634_v1.mrc as #58, grid size
400,400,400, pixel 1.24, shown at level 39.3, step 1, values float32  

> hide #!58 models

> hide #!57 models

> hide #!56 models

> hide #!55 models

> hide #!1 models

> show #!50 models

> hide #51 models

> hide #!50 models

> ui tool show "Surface Color"

> color sample #54.1 map #58 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56  

> color single #54.1

> color sample #54.1 map #58 palette 2.735,#ff0000:4,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56  

> color single #54.1

> color sample #54.1 map #58 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56  

> close #54

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2634_009_volume_map.mrc"

Opened cryosparc_P126_J2634_009_volume_map.mrc as #54, grid size 400,400,400,
pixel 1.24, shown at level 0.224, step 1, values float32  

> show #!58 models

> hide #!58 models

> color sample #54.1 map #58 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.735, mean 3.894, maximum 29.02  

> color single #54.1

> color sample #54.1 map #56 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 0.5331, maximum 17.84  

> close #54-58

> show #51 models

> show #!1 models

> view view9

Expected an objects specifier or a view name or a keyword  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4486_map_locres.mrc"

Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32  

> hide #!54 models

> color sample #1.1 map #54 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 2,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 1,#ff0000:10,#ffffff:20,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 3,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 4,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color sample #1.1 map #54 palette 1,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> color single #1.1

> color sample #1.1 map #54 palette 1,#ff0000:20,#ffffff:50,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> key red-white-blue :1 :20 :50 showTool true

> ui mousemode right "color key"

> color sample #1.1 map #54 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84  

> key red-white-blue :7.5 :35.2 :62.8 showTool true

> ui mousemode right "color key"

> color single #1.1

> color sample #1.1 map #48 palette 7.493,#ff0000:35.17,#ffffff:62.84,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :2.58 :5.15 :7.72 showTool true

> ui mousemode right "color key"

> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :2.5 :5.1 :7.7 showTool true

> ui mousemode right "color key"

> hide #51 models

> hide #!1 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2586_007_volume_map.mrc"

Opened cryosparc_P126_J2586_007_volume_map.mrc as #55, grid size 300,300,300,
pixel 1.24, shown at level 0.227, step 1, values float32  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J4484_map_locres_J2586.mrc"

Opened cryosparc_P126_J4484_map_locres_J2586.mrc as #56, grid size
300,300,300, pixel 2.48, shown at level 7.7, step 1, values float32  

> hide #!56 models

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579  

> color sample #55.1 map #56 palette 0,#ff0000:4.79,#ffffff:9.579,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579  

> color single #55.1

> close #56

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2953_map_locres_v2.mrc"

Opened cryosparc_P126_J2953_map_locres_v2.mrc as #56, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32  

> color sample #55.1 map #56 palette 0,#ff0000:4.79,#ffffff:9.579,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> hide #!55 models

> show #!55 models

> hide #!56 models

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color single #55.1

> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7.5,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color single #55.1

> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 0,#ff0000:3.642,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 2.5,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283  

> volume #55 level 0.1387

> volume #55 level 0.2647

> volume #56 level 5.608

> hide #!56 models

> volume #55 level 0.196

> color sample #55.1 map #56 palette 2,#ff0000:3,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette 2,#ff0000:5,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette 2,#ff0000:3.5,#ffffff:7.283,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> key red-white-blue :2.00 :3.50 :7.28 showTool true

> ui mousemode right "color key"

> show #51 models

> color sample #55.1 map #56 palette 2,#ff0000:3.5,#ffffff:6,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7.2,#0000ff
> outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19  

> close #55

> close #56

> hide #51 models

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Final maps and
> model/job073_local_res_filtered_map/relion_locres_filtered.mrc"

Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.00473, step 1, values float32  

> select add #55

2 models selected  

> show #!1 models

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models #55,1,0,0,-49.466,0,1,0,19.546,0,0,1,-35.582

> view matrix models #55,1,0,0,-125.29,0,1,0,-27.177,0,0,1,-72.202

> view matrix models #55,1,0,0,-131.08,0,1,0,-78.985,0,0,1,-39.391

> ui mousemode right "rotate selected models"

> view matrix models
> #55,-0.38231,0.6929,0.61133,-29.962,0.21577,0.71024,-0.67007,84.421,-0.89849,-0.12426,-0.42104,593.37

> view matrix models
> #55,-0.86508,-0.091241,-0.49327,551.34,0.025332,-0.99001,0.1387,320.67,-0.501,0.10749,0.85875,116.81

> ui mousemode right "translate selected models"

> view matrix models
> #55,-0.86508,-0.091241,-0.49327,563.32,0.025332,-0.99001,0.1387,328.73,-0.501,0.10749,0.85875,49.963

> view matrix models
> #55,-0.86508,-0.091241,-0.49327,502.1,0.025332,-0.99001,0.1387,335.45,-0.501,0.10749,0.85875,10.384

> ui mousemode right "rotate selected models"

> view matrix models
> #55,-0.7625,0.17437,-0.62305,444.83,-0.32722,-0.93469,0.13888,425.79,-0.55814,0.30977,0.76975,3.7603

> ui mousemode right "translate selected models"

> view matrix models
> #55,-0.7625,0.17437,-0.62305,440.55,-0.32722,-0.93469,0.13888,403.93,-0.55814,0.30977,0.76975,-7.0818

> fitmap #55 inMap #1

Fit map relion_locres_filtered.mrc in map W20_J3623_consensus_structure.mrc
using 248012 points  
correlation = 0.446, correlation about mean = 0.2993, overlap = 121.7  
steps = 328, shift = 23.5, angle = 15 degrees  
  
Position of relion_locres_filtered.mrc (#55) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.64805723 0.29760230 -0.70103830 399.38555473  
-0.32266507 -0.94108474 -0.10122635 486.21101125  
-0.68986164 0.16060010 0.70590263 74.18713432  
Axis 0.38883752 -0.01659842 -0.92115682  
Axis point 261.23669220 207.73357377 0.00000000  
Rotation angle (degrees) 160.32536182  
Shift along axis 78.88777001  
  

> select subtract #55

Nothing selected  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Final maps and model/Model_files/COPI_GOLPH3_combined_model_v14.mmcif"

Summary of feedback from opening /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Final maps and
model/Model_files/COPI_GOLPH3_combined_model_v14.mmcif  
---  
warnings | Unknown polymer entity '1' on line 142  
Unknown polymer entity '2' on line 206  
Unknown polymer entity '3' on line 1183  
Unknown polymer entity '4' on line 3547  
Unknown polymer entity '5' on line 4479  
11 messages similar to the above omitted  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for COPI_GOLPH3_combined_model_v14.mmcif #56  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
R S T | No description available  
  

> hide #!56 atoms

> show #!56 cartoons

> show #!24 models

> hide #!24 models

> select add #56

17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected  

> view matrix models #56,1,0,0,-57.326,0,1,0,-94.635,0,0,1,-152.05

> view matrix models #56,1,0,0,-96.675,0,1,0,-128.13,0,0,1,-110.53

> hide #!1 models

> color #55 #929292ff models

> color #55 #92929240 models

> view matrix models #56,1,0,0,-87.633,0,1,0,-75.202,0,0,1,-105.19

> ui mousemode right "rotate selected models"

> view matrix models
> #56,-0.57627,0.2909,-0.76373,403.39,-0.3025,-0.94406,-0.13134,514.31,-0.75921,0.15534,0.63203,127.54

> ui mousemode right "translate selected models"

> view matrix models
> #56,-0.57627,0.2909,-0.76373,414.45,-0.3025,-0.94406,-0.13134,516.62,-0.75921,0.15534,0.63203,106.07

> view matrix models
> #56,-0.57627,0.2909,-0.76373,421.71,-0.3025,-0.94406,-0.13134,495.85,-0.75921,0.15534,0.63203,110.7

> fitmap #56 inMap #55

Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms  
average map value = 0.005565, steps = 148  
shifted from previous position = 12.3  
rotated from previous position = 7.06 degrees  
atoms outside contour = 9511, contour level = 0.0047295  
  
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
0.99861221 0.04491552 0.02749984 -28.06097041  
-0.04715481 0.99508491 0.08707710 -7.47857239  
-0.02345356 -0.08825301 0.99582194 24.76832483  
Axis -0.85742564 0.24917997 -0.45025617  
Axis point 0.00000000 330.55403154 136.14787847  
Rotation angle (degrees) 5.86829908  
Shift along axis 11.04459412  
  

> select subtract #56

Nothing selected  

> select add #56

17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected  

> view matrix models
> #56,-0.64475,0.3289,-0.69002,379.8,-0.27547,-0.94202,-0.19162,491.22,-0.71303,0.066527,0.69797,103.59

> fitmap #56 inMap #55

Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms  
average map value = 0.005776, steps = 92  
shifted from previous position = 4.45  
rotated from previous position = 3.4 degrees  
atoms outside contour = 9140, contour level = 0.0047295  
  
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
0.99783486 0.06315960 -0.01834221 -2.15609454  
-0.06052615 0.99097184 0.11963015 -14.59510136  
0.02573241 -0.11826095 0.99264907 30.83542514  
Axis -0.87549404 -0.16220473 -0.45519206  
Axis point 0.00000000 213.68284829 151.38980884  
Rotation angle (degrees) 7.80841410  
Shift along axis -9.78099817  
  

> view matrix models
> #56,-0.68271,0.33689,-0.6484,381.54,-0.26761,-0.941,-0.20715,505.03,-0.67992,0.032098,0.73258,104.14

> fitmap #56 inMap #55

Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms  
average map value = 0.01255, steps = 84  
shifted from previous position = 7.68  
rotated from previous position = 7.81 degrees  
atoms outside contour = 1181, contour level = 0.0047295  
  
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:  
Matrix rotation and translation  
0.99999995 0.00017955 -0.00021830 0.02553185  
-0.00017956 0.99999997 -0.00007215 0.05642662  
0.00021829 0.00007219 0.99999997 -0.06358059  
Axis 0.24739544 -0.74829798 -0.61550437  
Axis point 282.18300475 0.00000000 113.24807650  
Rotation angle (degrees) 0.01671451  
Shift along axis 0.00322666  
  

> select subtract #56

Nothing selected  

> color #56/a label_purple_v3

> color #56/b label_purple_v3

> color #56/d navy

> color #56/e navy

> color #56/f betapv3

> color #56/g betapv3

> color #56/h betav1

> color #56/i betav1

> color #56/j betav1

> color #56/k betav1

> color #56/l deltav1

> color #56/l deltav3

> color #56/m gammav3

> color #56/n gammav3

> color #56/o gammav3

> color #56/s arf1v3

> color #56/r arf1v3

> color #56/t arf1v3

> hide #!56 models

> hide #!55 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

> show #!24 models

> select add #24.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #24.13

Nothing selected  

> select add #25.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #25.13

Nothing selected  

> hide #!24 models

> show #!26 models

> select add #26.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #26

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #26

Nothing selected  

> show #!27 models

> select add #26.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> select add #26

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #26

Nothing selected  

> select add #27.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #27

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #27

Nothing selected  

> hide #!26 models

> hide #!27 models

> select add #28.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #28.13

Nothing selected  

> select add #29.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select add #29

27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected  

> select subtract #29

Nothing selected  

> select add #30.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #30.13

Nothing selected  

> select add #32.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #32.13

Nothing selected  

> show #!33.13 models

> select add #33.13

2744 atoms, 2786 bonds, 1 pseudobond, 354 residues, 2 models selected  

> color sel gammav3

> select subtract #33.13

Nothing selected  

> show #34.13 models

> select add #34.13

4552 atoms, 4624 bonds, 582 residues, 1 model selected  

> color sel gammav3

> select subtract #34.13

Nothing selected  

> hide #!33 models

> hide #!34 models

> show #!33 models

> hide #!33 models

> show #!35 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!39 models

> hide #!39 models

> show #!40 models

> hide #!40 models

> show #!41 models

> hide #!41 models

> show #!42 models

> hide #!42 models

> show #!43 models

> hide #!43 models

> show #!44 models

> hide #!44 models

> show #!45 models

> hide #!45 models

> show #!46 models

> hide #!46 models

> show #!47 models

> hide #!47 models

> show #!49 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!49 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

> show #!55 models

> show #!56 models

> view view1

> view view2

> view view3

> view view4

> view view5

> view view6

Expected an objects specifier or a view name or a keyword  

> view view7

Expected an objects specifier or a view name or a keyword  

> view view8

Expected an objects specifier or a view name or a keyword  

> volume #55 level 0.0055

> volume #55 level 0.005

> color #55 darkgrey models

> color #55 #929292ff models

> color #55 #92929267 models

> ui tool show "Side View"

> view name view8

> hide #!56 models

> hide #!55 models

> show #!50 models

> show #!47 models

> color #47 #929292ff models

> color #47 #92929266 models

> ui mousemode right select

> select clear

[Repeated 2 time(s)]

> hide #!50 models

> show #!50 models

Drag select of 2 residues  

> select up

166 atoms, 167 bonds, 24 residues, 1 model selected  

> delete sel

Drag select of 7 residues  

> select up

149 atoms, 150 bonds, 18 residues, 1 model selected  

> delete sel

> select #50/L:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #50/L:2

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> select #50/L:3

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete sel

> select #50/L:4

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #47

3 models selected  

> select clear

> select #50/L:5

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> hide #!50 models

> show #!49 models

> hide #!47 models

> show #!46 models

> select #49/L:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> \

Unknown command: \  

> delete sel

> select #46

2 models selected  

> select clear

> select #46

2 models selected  

> hide #!46 models

> select subtract #46

Nothing selected  

> select #49/L:2

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete sel

> select #49/L:3

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete sel

> show #!46 models

> select #49/L:4

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

> select #49/L:5

8 atoms, 7 bonds, 1 residue, 1 model selected  

> delete sel

Drag select of 3 residues  

> select up

149 atoms, 150 bonds, 18 residues, 1 model selected  

> delete sel

> select clear

[Repeated 1 time(s)]Drag select of 4 residues  

> select up

166 atoms, 167 bonds, 24 residues, 1 model selected  

> delete sel

> hide #!49 models

> hide #!46 models

> color #46 #929292ff models

> color #46 #92929266 models

> show #!46 models

> show #!49 models

> view view8

> hide #!49 models

> hide #!46 models

> show #!55 models

> show #!56 models

> view name view8

> hide #!56 models

> hide #!55 models

> show #!50 models

> show #!47 models

> volume #47 level 4.58

> view view8

> hide #!50 models

> hide #!47 models

> show #!56 models

> show #!55 models

> hide #!56 models

> hide #!55 models

> show #!55 models

> show #!46 models

> hide #!46 models

> show #!46 models

> color #55 #d4fb79ff models

> select add #55

3 models selected  
Drag select of 46 composite_map_J4021_J4026.ccp4 , 55
relion_locres_filtered.mrc  

> select add #55

5 models selected  

> select subtract #55

2 models selected  

> ui mousemode right "translate selected models"

> select add #55

5 models selected  

> select subtract #55

2 models selected  

> select add #46

3 models selected  

> select subtract #46

Nothing selected  

> select add #55

3 models selected  

> view matrix models
> #55,-0.64806,0.2976,-0.70104,404.74,-0.32267,-0.94108,-0.10123,483.04,-0.68986,0.1606,0.7059,77.297

> ui mousemode right "rotate selected models"

> view matrix models
> #55,-0.73178,0.069047,-0.67804,474.38,-0.12094,-0.99222,0.029485,404.07,-0.67073,0.10358,0.73444,77.507

> fitmap #55 inMap #1

Fit map relion_locres_filtered.mrc in map W20_J3623_consensus_structure.mrc
using 191343 points  
correlation = 0.5091, correlation about mean = 0.3117, overlap = 135.7  
steps = 196, shift = 24.8, angle = 11.2 degrees  
  
Position of relion_locres_filtered.mrc (#55) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.75253459 0.06710395 -0.65512499 473.61243410  
0.00933094 -0.99360872 -0.11249292 428.86098374  
-0.65848662 -0.09076775 0.74709878 117.70957595  
Axis 0.35145885 0.05438278 -0.93462249  
Axis point 262.44867657 214.17046526 0.00000000  
Rotation angle (degrees) 178.22886921  
Shift along axis 79.76391490  
  

> select subtract #55

Nothing selected  

> color #55 #929292ff models

> color #55 #92929266 models

> hide #!46 models

> view view8

> show #!56 models

> hide #!56 models

> hide #!55 models

> show #!50 models

> show #!47 models

> hide #!50 models

> hide #!47 models

> show #!49 models

> show #!46 models

> view name view8a

> hide #!49 models

> hide #!46 models

> show #!46 models

> show #!49 models

> view name view9

> hide #!49 models

> hide #!46 models

> show #!47 models

> show #!50 models

> hide #!50 models

> view name view10

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

——— End of log from Tue Jul 8 14:25:38 2025 ———

opened ChimeraX session  

> show #!1 models

> hide #!47 models

> view view1

> show #51 models

> ui tool show "Surface Color"

> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :2.5 :5.1 :7.7 showTool true

> ui mousemode right "color key"

> ui mousemode right "translate selected models"

> key red-white-blue :2.5 :5.0 :7.0 showTool true

> ui mousemode right "color key"

> key red-white-blue :2.5 :5.0 :7.0

> ui mousemode right "translate selected models"

> color sample #1.1 map #48 palette 2.5,#ff0000:5,#ffffff:7,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> view view1

> view view2

> view view3

> view view4

> view view5

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff

Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72  

> key red-white-blue :3 :5 :8 showTool true

> ui mousemode right "color key"

> ui mousemode right "translate selected models"

> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/chimerax_images/J3623_consensus_view5_locales_color_v2.png
> width 866 height 597 supersample 3 transparentBackground true

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/J3740_betaprime_3Dclass/J3740_betaprime_3Dclass_aligned.py"

Failed opening file /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/Processing/Files from
csparc/J3740_betaprime_3Dclass/J3740_betaprime_3Dclass_aligned.py:  
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to  
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene  
menu item, and change the resulting dialog's "File Type" to ChimeraX.  

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"

——— End of log from Tue Jul 8 14:43:14 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!1 models

> hide #51 models

> show #!6 models

> volume #6 level 0.198

> color #6 darkgrey models

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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4021_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!6 models

> show #!8 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4022_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> color #8 #797979ff models

> show #!6 models

> color #6 #d6d6d6ff models

> color #6 silver models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4021_J4022_betaprime_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true

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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4023_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!10 models

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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4024_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!12 models

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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4025_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!14 models

> show #!12 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4024_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4023_J4024_J4025_betaprime_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true

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[Repeated 1 time(s)]

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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4026_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!16 models

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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4027_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!18 models

> show #!20 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4028_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!20 models

> show #!22 models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J3988_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!22 models

> show #!20 models

> show #!18 models

> show #!16 models

> show #!22 models

> hide #!22 models

> hide #!20 models

> color #16 silver models

> color #16 #919191ff models

> color #18 #d6d6d6ff models

> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4027_J4026_gammazeta_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true

> hide #!18 models

> hide #!16 models

> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250709_W20_COPI_cyto_alignments.cxs"

——— End of log from Wed Jul 9 09:46:30 2025 ———

opened ChimeraX session  

> show #!49 models

> hide #!49 models

> show #!50 models

> show #!49 models

> hide #!49 models

> hide #!50 models

> ui tool show XMAS

Traceback (most recent call last):  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S000N6D/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.6 (23H626)
      Kernel Version: Darwin 23.6.0
      Time since boot: 6 days, 18 hours, 15 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    biopython: 1.85
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.6.0
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-locscalesurfer: 0.1.1
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.7
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 2.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RIBFIND: 0.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
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    cxservices: 1.2.3
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    Cython: 3.0.10
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    decorator: 5.1.1
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    et_xmlfile: 2.0.0
    executing: 2.1.0
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    fsspec: 2025.5.1
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    geomdl: 5.3.1
    glfw: 2.8.0
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    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
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    importlib_resources: 6.4.0
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    ipython: 8.26.0
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    jaraco.functools: 4.0.1
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    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
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    nptyping: 2.5.0
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    numpy: 1.26.4
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    packaging: 23.2
    packaging: 24.1
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    ParmEd: 4.2.2
    parso: 0.8.4
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    pillow: 10.4.0
    pip: 24.2
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    platformdirs: 4.2.2
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    pydantic_core: 2.33.0
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    PyOpenGL-accelerate: 3.1.7
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    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
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    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
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    QtPy: 2.4.2
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    qtshim: 1.0
    RandomWords: 0.4.0
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    ribfind: 2.0.2
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    typing_extensions: 4.12.2
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    webcolors: 24.6.0
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    wheel: 0.43.0
    wheel-filename: 1.4.1
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